189
Supplementary Online Material SGA Analysis: Robotic Manipulation of Yeast Arrays The robotic manipulation of deletion mutant array (DMA) and SGA screens were carried out as described (S1). We conducted each SGA screen three times and scored the resultant double mutants for synthetic genetic interactions by both visual inspection and computer-based image analysis. The computer-based scoring generated an estimate of relative growth rates from the area of individual colonies, as measured from digital images of the growth plates. A comparison of a set of mutant measurements to wild-type control measurements enabled t-statistics and p-values to be calculated (S2). For each screen, we generated both an unbiased set of putative interactions and a biased set of putative interactions. The unbiased set included double mutants that appeared to form a relatively small colony by the computer-based system, i.e. scored at a t-value of -7.0 or less, and those that were scored repeatedly by visual inspection. The biased set included double mutants that were either scored above a t-value of -7.0 or scored only once by visual inspection but were also related functionally to multiple genes within the unbiased set. To represent gene function, we assigned each gene a GO functional annotation from a defined subset (Table S8). The putative synthetic genetic interactions were confirmed by random spore and/or tetrad analysis. Sporulated cultures from SGA screens were stored at 4 o C for the confirmation. Tetrad dissections were carried out on synthetic dextrose (SD/MSG) complete medium. We dissected tetrads for interactions that appeared to be inconclusive in the random spore assay. SGA Analysis: Media The media used in the SGA analysis were described previously (S1). Because ammonium sulfate impedes the function of G418 and clonNAT, synthetic medium containing these antibiotics was made with monosodium glutamic acid (MSG) as a nitrogen source; for selection of MATa meiotic progeny, the medium lacked histidine (selects for expression of MFA1pr-HIS3) and contained canavanine (selects for can1) [20g/L agar, 20g/L glucose, 1.7g/L yeast nitrogen base w/o ammonium sulphate and amino acids (Difco), 1g/L monosodium glutamic acid, 2g/L amino acid drop-out lacking histidine and arginine]. Filtered-sterilized solutions of canavanine (50mg/l; Sigma), clonNAT (100mg/l; Werner Bioagents), and G418 (200mg/l; Invitrogen Life Technologies) were added to autoclaved medium as indicated. Solid medium contained 2% agar. (SD/MSG) – His/Arg + canavanine; (SD/MSG) – His/Arg + canavanine/clonNAT; (SD/MSG) – His/Arg + canavanine/G418; (SD/MSG) – His/Arg + canavanine/clonNAT/G418 were used for random spore analysis. Synthetic dextrose (SD/MSG) complete medium was used for tetrad analysis. SGA Analysis: Starting Strains and Reporters All strains are derivatives of BY4741 (MATa ura30 leu20 his31 met150) or BY4742 (MATα ura30 leu20 his31 lys20) (S3). Four different starting strains were used in the SGA screens, Y2454 (MATα mfa1::MFA1pr-HIS3 can1ura30 leu20 his31 lys20), Y3068 (MATα can1::MFA1pr-HIS3 ura30 leu20 his31 lys20), Y3084 (MATα can1::MFA1pr-HIS3 mfα1::MFα1pr-LEU2 ura30 leu20 his31 lys20), the construction of which was described previously (S1), and Y3656 (MATα

Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

  • Upload
    others

  • View
    1

  • Download
    0

Embed Size (px)

Citation preview

Page 1: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

Supplementary Online Material SGA Analysis: Robotic Manipulation of Yeast Arrays

The robotic manipulation of deletion mutant array (DMA) and SGA screens were carried out as described (S1). We conducted each SGA screen three times and scored the resultant double mutants for synthetic genetic interactions by both visual inspection and computer-based image analysis. The computer-based scoring generated an estimate of relative growth rates from the area of individual colonies, as measured from digital images of the growth plates. A comparison of a set of mutant measurements to wild-type control measurements enabled t-statistics and p-values to be calculated (S2). For each screen, we generated both an unbiased set of putative interactions and a biased set of putative interactions. The unbiased set included double mutants that appeared to form a relatively small colony by the computer-based system, i.e. scored at a t-value of -7.0 or less, and those that were scored repeatedly by visual inspection. The biased set included double mutants that were either scored above a t-value of -7.0 or scored only once by visual inspection but were also related functionally to multiple genes within the unbiased set. To represent gene function, we assigned each gene a GO functional annotation from a defined subset (Table S8). The putative synthetic genetic interactions were confirmed by random spore and/or tetrad analysis. Sporulated cultures from SGA screens were stored at 4oC for the confirmation. Tetrad dissections were carried out on synthetic dextrose (SD/MSG) complete medium. We dissected tetrads for interactions that appeared to be inconclusive in the random spore assay. SGA Analysis: Media The media used in the SGA analysis were described previously (S1). Because ammonium sulfate impedes the function of G418 and clonNAT, synthetic medium containing these antibiotics was made with monosodium glutamic acid (MSG) as a nitrogen source; for selection of MATa meiotic progeny, the medium lacked histidine (selects for expression of MFA1pr-HIS3) and contained canavanine (selects for can1∆) [20g/L agar, 20g/L glucose, 1.7g/L yeast nitrogen base w/o ammonium sulphate and amino acids (Difco), 1g/L monosodium glutamic acid, 2g/L amino acid drop-out lacking histidine and arginine]. Filtered-sterilized solutions of canavanine (50mg/l; Sigma), clonNAT (100mg/l; Werner Bioagents), and G418 (200mg/l; Invitrogen Life Technologies) were added to autoclaved medium as indicated. Solid medium contained 2% agar. (SD/MSG) – His/Arg + canavanine; (SD/MSG) – His/Arg + canavanine/clonNAT; (SD/MSG) – His/Arg + canavanine/G418; (SD/MSG) – His/Arg + canavanine/clonNAT/G418 were used for random spore analysis. Synthetic dextrose (SD/MSG) complete medium was used for tetrad analysis. SGA Analysis: Starting Strains and Reporters

All strains are derivatives of BY4741 (MATa ura3∆0 leu2∆0 his3∆1 met15∆0) or BY4742 (MATα ura3∆0 leu2∆0 his3∆1 lys2∆0) (S3). Four different starting strains were used in the SGA screens, Y2454 (MATα mfa1∆::MFA1pr-HIS3 can1∆ ura3∆0 leu2∆0 his3∆1 lys2∆0), Y3068 (MATα can1∆::MFA1pr-HIS3 ura3∆0 leu2∆0 his3∆1 lys2∆0), Y3084 (MATα can1∆::MFA1pr-HIS3 mfα1∆::MFα1pr-LEU2 ura3∆0 leu2∆0 his3∆1 lys2∆0), the construction of which was described previously (S1), and Y3656 (MATα

Page 2: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

2

can1∆::MFA1pr-HIS3::MFα1pr-LEU2 ura3∆0 leu2∆0 his3∆1 lys2∆0). In Y2454, HIS3 was integrated at the MFA1 locus such that it is regulated by the MFA1 promoter (pr), mfa1∆::MFA1pr-HIS3. In Y3068, MFA1pr-HIS3 was integrated at the CAN1 locus, can1∆::MFA1pr-HIS3. In Y3084, MFA1pr-HIS3 was integrated at the CAN1 locus, can1∆::MFA1pr-HIS3 and MFα1pr-LEU2 was integrated at the MFα1 locus. In Y3656, MFA1pr-HIS3 was integrated 5’ to MFα1pr-LEU2 at the CAN1 locus.

To create Y2823 (MATα mfα1∆::MFα1pr-LEU2 his3∆1 leu2∆0 ura3∆0 lys2∆0) and Y3084, the MFα1 open reading frame was replaced by the LEU2 gene, via integration of a PCR product generated with primers (5’-CAAACAAGAAGATTACAAACTATCAATTTCATACACAATATAAACGATTAAAAGAATGTCTGCCCCTAAGAAGATCGC-3’) and (5’-TACAGTGGGAACAAAGTCGACTTTGTTACATCTACACTGTTGTTATCAGTCGGGCTTAAGCAAGGATTTTCTTAACTTC- 3’), which anneal to LEU2 and contained MFα1 sequences (underlined), with pRS315 plasmid as the template (S4), and transformed in BY4742 and Y3068 respectively.

The construction of Y3656 involved three steps. First, to create Y3598 (MATa can1∆::MFA1pr-HIS3::MFα1pr-LEU2 his3∆1 leu2∆0 ura3∆0 met15∆0) which carries can1∆::MFA1pr-HIS3::MFα1pr-LEU2, MFA1pr-HIS3::MFα1pr-LEU2 was integrated at the CAN1 locus. Second, Y3598 was crossed to BY4742 to create Y3611 (MATa/α can1∆::MFA1pr-HIS3::MFα1pr-LEU2/CAN1 his3∆1/ his3∆1 leu2∆0/ leu2∆0 ura3∆0/ ura3∆0 met15∆0/MET15 lys2∆0/LYS2). Third, the resulting MATa/α diploids were sporulated and spore progeny with the appropriate markers were recovered.

The construction of Y3598 involved four steps. First, a 455-bp fragment containing the upstream sequence of CAN1 was amplified from yeast genomic DNA with primers (5’-TAGGGCGAACTTGAAGAATAACC-3’) and (5’-GCCACGTTGCACACTATCCTGTGCTATGCCTTTTTTTTTTTTTGTT-3’), which contained a 21-bp sequence (underlined) from the 5’ end of MFA1pr-HIS3. Second, MFA1pr-HIS3 was amplified from genomic DNA obtained from Y2420 (MATa mfa1∆::MFA1pr-HIS3 ura3∆0 leu2∆0 his3∆1 met15∆0) with primers (5’-CAGGATAGTGTGCAACGTGGC-3’) and (5’-CTCATTGAATCTTTGCATTCAGAGCGTCTACATAAGAACACCTTTGGTGG-3’) which contained a 27-bp sequence (underlined) from the 5’ end of the MFα1pr-LEU2. Third, MFα1pr-LEU2 was amplified from genomic DNA obtained from Y2823 with primers (5’-ACGCTCTGAATGCAAAGATTCAATGAG-3’) and (5’-ATCAAAGGTAATAAAACGTCATATTTAAGCAAGGATTTTCTTAACTTC-3’) which contained a 24-bp sequence (underlined) from the 5’ end of the CAN1 downstream sequence. Fourth, a 300-bp fragment containing the CAN1 downstream sequence was amplified from yeast genomic DNA with primers (5’-ATATGACGTTTTATTACCTTTGAT-3’) and (5’-ACGAAAAATGAGTAAAAATTATCTT-3’). Finally, the set of PCR products above was used as a template to generate a fused product with primers (5’-TAGGGCGAACTTGAAGAATAACC-3’) and (5’-ACGAAAAATGAGTAAAAATTATCTT-3’). BY4741 transformants carrying can1∆::MFA1pr-HIS3::MFα1pr-LEU2 were selected on synthetic medium lacking histidine.

Page 3: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

3

SGA Analysis: Yeast Strains The construction of query strains Y2613 (bni1∆::URA3), Y2927 (bni1∆::natR), Y3029 (arc40-40::URA3), Y3121 (nbp2∆::natR), Y3122 (bbc1∆::natR), Y3181 (arp2-33::URA3), Y3304 (bim1∆::natR), Y3310 (sgs1∆::natR), Y3334 (rad27∆::natR) was described previously (S1). Construction of the following query strains was described previously: Y2928 (cla4∆::natR) (S5), Y4121 (cdc42-118::natR) (S6), Y4490 (set2∆::natR) (S7), Y4521 (elg1∆::natR) (S8), and pho85∆::natR (S9). The temperature-sensitive (t.s.) query strains carrying cdc7-1::URA3, cdc8-2::URA3, dbf4::URA3, cdc45-1::natR, cdc2-1::natR, and scc1-73::URA3 were constructed by PCR-based integration of the t.s. alleles into Y2454 as described previously (S1). The t.s. query strain carrying myo2-14::LEU2 was constructed by PCR-based integration in Y3068. PCR-based deletion was used to create the following strains in starting strain Y2454: rvs161∆::natR, rvs167∆::natR, slt2∆::natR, ycr030c∆::natR, ygr221c∆::natR, yhr149c∆::natR, and gyp1∆::natR. PCR-based deletion was used to create the following strains in starting strain Y3656: dep1∆::natR, cti6∆::natR, and om45∆::natR. We used a switcher/replica-plating method (S1) to create the following query strains with the SGA starting strain Y3084: rad9∆::natR, ydr063w∆::natR, gim3∆::natR, elp2∆::natR, pac10∆::natR, rad24∆::natR, yke2∆::natR, rad52∆::natR, yor271c∆::natR, ddc1∆::natR, pol32∆::natR, mms4∆::natR, ybr094w∆::natR, mus81∆::natR, cdc73∆::natR, bni4∆::natR, num1∆::natR, ypt6∆::natR, nip100∆::natR, bik1∆::natR, arp6∆::natR, kar3∆::natR, kar9∆::natR, gim4∆::natR, ric1∆::natR, ase1∆::natR, elp4∆::natR, alg6∆::natR, alg8∆::natR, chs1∆::natR, chs5∆::natR, chs7∆::natR, cne1∆::natR, cts1∆::natR, cwh41∆::natR, die2∆::natR, fks1∆::natR, fks3∆::natR, gas1∆::natR, gsc2∆::natR, hkr1∆::natR, hoc1∆::natR, hog1∆::natR, knh1∆::natR, kre1∆::natR, kre11∆::natR, kre6∆::natR, ktr2∆::natR, ktr3∆::natR, lag2∆::natR, mid2∆::natR, mnl1∆::natR, mns1∆::natR, rot2∆::natR, skn1∆::natR, skt5∆::natR, smi1∆::natR, yur1∆::natR.

We used the switcher/replica-plating method (S1) to create the following strains with the SGA starting strain Y3656: jnm1∆::natR, arp1∆::natR, shs1∆::natR, smy1∆::natR, cin8∆::natR, bfa1∆::natR, ctf8∆::natR, cin2∆::natR, yor022c∆::natR, ycl039w∆::natR, ydr128w∆::natR, tub3∆::natR, dyn2∆::natR, dyn1∆::natR, mrc1∆::natR, pac1∆::natR, dcc1∆::natR, hst1∆::natR, esc2∆::natR, hst3∆::natR, rad50∆::natR, rad61∆::natR, rtt107∆::natR, mlc2∆::natR, clb4∆::natR, ras2∆::natR, gim5∆::natR, pxl1∆::natR, mad2∆::natR, ctf4∆::natR, tof1∆::natR, ydr332w∆::natR, lia1∆::natR, kip3∆::natR, csm3∆::natR, elg1∆::natR, cin4∆::natR, top1∆::natR, cin1∆::natR, pac2∆::natR, rrm3∆::natR, rbl2∆::natR, pac11∆::natR, kip2∆::natR, ypl225w∆::natR, ctf18∆::natR, chl1∆::natR, arl3∆::natR, hpr5∆::natR, elp1∆::natR, arl1∆::natR, ymr299c∆::natR, sap30∆::natR, swf1∆::natR, ykl151c∆::natR, yil103w∆::natR, yer156c∆::natR, ydl038c∆::natR, ynl087w∆::natR, bph1∆::natR, chs3∆::natR, chs6∆::natR, ecm15∆::natR, erv29∆::natR, hlr1∆::natR, kre2∆::natR, kre9∆::natR, las21∆::natR, lre1∆::natR, svp26∆::natR, ykl037w∆::natR, ylr057w∆::natR.

Page 4: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

4

The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed in two steps. First, Y2613 (MATα bni1∆::URA3) was crossed to a MATa bim1∆::natR strain. Second, the resulting MATa/α diploids were sporulated, and spore progeny with the appropriate markers were recovered. The double-mutant query strain bni1∆::URA3 kre1∆::natR was constructed using the switcher/replica-plating method (S1). SGA Analysis: Random Spore Analysis Spores were inoculated in 3ml of liquid haploid selection medium [synthetic dextrose (SD) medium lacking histidine and arginine but containing canavanine :SD - His/Arg + canavanine] and incubated at 30oC for 2 days. The germinated MATa spore progeny were diluted in sterile ddH2O and plated out on medium which selects for the query-gene mutation [(SD/MSG) – His/Arg + canavanine/clonNAT], the DMA mutation [(SD/MSG) – His/Arg + canavanine/G418], or both the query-gene and DMA mutations [(SD/MSG) – His/Arg + canavanine/clonNAT/G418], then incubated at 30oC for ~2 days. Colony growth under the three conditions was compared and the double mutants were scored as synthetic sick (SS), synthetic lethal (SL) or no interaction (No).

Alternatively, spores were resuspended in sterile ddH2O and plated out on the haploid selection medium [SD-His/Arg + canavanine] and medium selecting for the query-gene mutation, the DMA mutation, and both the query-gene and DMA mutations, then incubated at 30oC for ~2 days. Colony growth under the four conditions was compared and double mutants were scored as synthetic sick (SS), synthetic lethal (SL) or no interaction (No). SGA Analysis: Spot Assay Version of Random Spore Analysis

We applied a spot assay version of the random spore analysis procedure when examining neighborhood topology of SGS1, RAD27 and BIM1. First, spores were inoculated into liquid haploid selection medium [SD-His/Arg + canavanine] and incubated at 30oC for ~2 days in a 96-well format. Second, the germinated MATa spore progeny were diluted to 10-2, 10-4, and 10-6 in sterile ddH2O and 2µl for each dilution was spotted onto medium selecting for the query-gene mutation, the DMA mutation, and both the query-gene and DMA mutations, as described above, then incubated at 30oC for ~2 days. Cell growth under the three conditions was compared; double mutants were scored “Yes” for those that exhibited a synthetic genetic interaction or “No” for those that did not show an enhanced growth defect over the single mutants (Fig. S7). Network Visualization Programs Network figures were created with either the Cytoscape network layout program (S10) using manual alterations to remove node overlap and to cluster the nodes by cellular role, or the Osprey program (version 0.9.10) using a spokes layout. We colored the nodes according to our set of defined GO annotations (Table S8). Two-dimensional Hierarchical Agglomerative Clustering The Hierarchical Agglomerative clustering method was performed on the data. To determine the distance between nodes (i.e. clusters, sub-clusters, and individual interactions) we used Average Linkage, wherein the distance between the averages of the

Page 5: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

5

points in each node was the distance between two nodes. The distance metric is called the Binary metric and is defined as below. The Binary Metric: NOTE: in the Binary metric, two items are considered to match if both are either zero or non-zero. This metric ignores magnitude, thus the name “Binary”. Let X and Y be two distinct queries, and let Xi and Yi be individual experiment results for X and Y respectively. Let A be the set of all experiments in which Xi and Yi do not match and Yi is non-zero. Let B be the set of all experiments in which Xi and Yi do not match and Xi is non-zero. Let C be the set of all experiments in which Xi and Yi do match and are non-zero. Let D be the set of all experiments in which Xi and Yi do match and zero. Thus, Ai, Bi, Ci and Di are as follows: Ai Bi Ci Di Xi 0 1 1 0 Yi 1 0 1 0 The distance between the result vectors for X and Y is: (|A| + |B|) / (|A| + |B| + |C|) Analysis of the Potential for False Negative Interactions Because of the huge number of interactions involved, it is not feasible to confirm all putative interactions by tetrad or random spore analysis; therefore, the true number of false negative interactions is not known. In an effort to better understand the statistical properties of the raw SGA results, we developed a computer-based quantitative system to describe the growth rate of all colonies from measurements of colony area from digital images of growth plates. Synthetic lethal or sick interactions were scored based on calibration variables such as the growth of colonies and the values of t-statistics and p-values, which were calculated by comparison to a set of wild-type control measurements. The number of false negative interactions can be estimated as a function of the calibration variable (Fig. S1 and S2). Complete SGA screens include the genes in both bait and prey lists, thus should provide a symmetric matrix of data. The following table shows the possible cases of reciprocal crosses between baits and preys.

A true positive exists when both hits (A,B) and (B,A) are confirmed positive and a false negative exists when (A,C) is confirmed positive but (C,A) is not (or the reverse case). In the SGA experiment, 104 screens are present where the bait gene was found as a hit in any other screen. In an effort to

examine the false negative rate of this large subset of the SGA data set, we counted the number of false negative cases and compared that to the total. There are 990 interactions found in both directions, which include both cases of (bait, prey) and (prey, bait) and 266 without reciprocal interactions. This means another 266 hits were missed as false negatives, assuming that all these hits are true positives. In other terms, 990+266=1256

A B C A + + B + - C -

Page 6: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

6

interactions were seen out of an expected number of 990+266+266=1522 true positives, suggesting a false negative rate of about 17%. Network Density We compared the network density (ratio of number of interactions to number of nodes) of the SGA network and the protein interaction network. The SGA technique has an average of 34.4 interactions per screen. There is a maximum of 146 interactions and a minimum of 1 interaction per SGA screen. After examining various protein interaction datasets (see Table S2), we decided to use the TAP and HMS-PCI datasets as a comparison because they are the most recent published large-scale interaction mapping experiments for yeast. We determined that the density of the SGA network is ~4 times more than the protein interaction network (34.4/8=~4). This is likely to be a low estimate, since the SGA screens are expected to have a certain false negative rate and the protein interactions screens are known to have a large false-positive rate. Abandoned Screens Approximately 20% of the screens we attempted did not appear to yield any interactions and were aborted after the first SGA screen. The criteria we used for determining if a SGA screen is worth pursuing included the number of putative interactions scored (>50 interactions) and common functionality among the putative interactions identified. The screens aborted after the first SGA screen involved query mutations in BPH1, ELP1, ELP2, ELP4, FKS3, HLR1, KRE2, KTR2, LAG2, MLC2, OM45, PXL1, RAD61, YCL039w, YCR030c, YDL038c, YDR063w, YDR128w, YER156c, YGR221c, YHR149c, YIL103w, YKL151c, YNL087w, YOR022c, YOR271c, YPL225w. Pre-processing the Genetic Interactions Network for Computational Analysis The analysis shown in Table S3, analysis of “genetically connected” GO attributes, and the analysis of degree distribution and characteristic path length, used the following protocol for pre-processing the genetic network: 1) ORFs corresponding to the same SGDID were merged, with an interaction to one or both of the merged gene objects treated subsequently as an interaction with the merged gene; 2) ORFs that were listed as "deleted" in SGD were removed from the genetic interaction network, which did not require removal of any genetic interactions but did affect which pairs were considered SGA-tested; 3) all gene pairs containing query genes that were tested by a single SGA screen but subsequently abandoned for lack of hits were considered tested and non-interacting. For the analysis shown in Table S3 and the search for “genetically connected” GO functional attributes, each of which might be affected by an increased sensitivity of SGA to detect functionally-related genes, we applied two additional pre-processing steps: 1) a gene pair was considered non-interacting if confirmation of the interaction was attempted on the basis of gene function and if this gene pair would otherwise have been deemed non-interacting; and 2) any SGA gene not tested against all query genes was removed from the network, along with any interactions connected to that SGA gene. Gene-Pair Characteristics and Their Data Sources

Page 7: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

7

Common Regulator Pairs of genes whose upstream regions bind a common transcription factor were collected from a high-throughput data set in which DNA bound by a query transcription factor was hybridized to an array of upstream sequences (S11). Genes whose upstream regions yielded p-values < 0.001 were considered bound by the associated transcription factor. Conserved Gene Neighborhood Pairs of genes that are next to each other in at least 2 of 42 genomes were collected from von Mering et al. (S12). Co-occurrence of Genes Pairs of genes whose orthologs have correlated appearance across 42 sequenced genomes were collected from von Mering et al. (S12). Gene Fusion Gene pairs each contained genes that were orthologous to separate domains of a common gene in another species. Gene fusions were detected by the presence of a gene in more than one Cluster of Orthologous Genes (COG) and were collected (S13). mRNA Co-expression Pairs of genes with correlated mRNA expression were collected from two data sets, 1) mRNA expression in the yeast mitotic cell cycle measured at 17 time-points in synchronized yeast cultures (S14) and 2) the Rosetta compendium of mRNA expression profiles drawn from a variety of growth conditions and strain backgrounds (S15). For each gene, all mRNA levels were converted to log-ratios and standardized to a common mean and variance. We computed the Pearson correlation coefficient between all gene pairs to measure the similarity in expression profiles. We considered gene pairs with positive (>0.7) and negative correlations (<0.7) in their mRNA expression profiles. Mutual Clustering Coefficient Pairs of genes with a high mutual clustering coefficient (MCC), a measure of neighborhood cohesiveness around an edge (or pair of vertices) in a graph of physical protein interactions, were collected. The MCC is the negative log of the probability (p-value) of obtaining a number of common neighbors between two vertices greater than or equal to the observed number by chance, under the null hypothesis that the neighborhoods are independent and given the neighborhood sizes of the two vertices and the total number of proteins in the organism (S16). We computed MCC for a network including yeast-two-hybrid (Y2H) interactions reported by Uetz et al. (S17) and the high-confidence Y2H interactions reported by Ito et al. (S18). MCC thresholds of >0 and >3 were used to create to categories of gene pairs with high MCC. Physical Interaction: APMS Pairs of proteins detected to interact by tandem affinity purification (TAP) (S19), by high-throughput mass spectrometric protein complex identification (HMS-PCI) (S20), or by both methods. These methods were based on affinity purification followed by mass spectroscopy (APMS).

Page 8: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

8

Physical Interaction: HMS-PCI Pairs of proteins were detected to physically interact by high-throughput mass spectrometric protein complex identification (HMS-PCI) (S20). Two data sets were constructed based on the filtered data obtained from http://www.mdsp.com/yeast/. The “spoke” (S21) interactions included interactions between a query protein, or bait, and proteins that complexed with it. The “matrix” (S21) interactions included all pairwise interactions represented in a purified complex obtained when using a single bait. Physical Interaction: Same MIPS Complex (annotated in the literature) Gene pairs were generated from complexes reported in the MIPS catalog of complexes (S12). Physical Interaction: TAP Protein pairs were detected to physically interact by the tandem affinity purification (TAP) and mass spectrometry experiments of Gavin et al. (S19). We collected two datasets based upon all purifications, excluding proteins that appeared in more than 3.5% of the purifications. The “spoke” (S21) interactions included interactions between a query protein, or bait, and all proteins that complexed with it. The “matrix” (S21) interactions included all pairwise interactions represented in a purified complex obtained when using a single bait. Physical Interaction: Yeast-Two-Hybrid (YTH) Interacting gene pairs were assembled from previous high-throughput yeast-two-hybrid results. These consisted of two independent yeast-two-hybrid data sets, described by Ito (S18) and Uetz (S17), respectively. The Ito and Uetz data sets were obtained from http://genome.c.kanazawa-u.ac.jp/Y2H/ and http://depts.washington.edu/sfields/yplm/data/index.html, respectively. Protein Sequence Homology Yeast mRNAs were collected (July 2002) from RefSeq (S22) translated, and BLASTed (S23) against each other. Pairs with E-values below 10-3 were considered homologous. Same GO Annotation Pairs in which both genes are annotated with identical specific Gene Ontology (GO) terms were collected from the Gene Ontology (S24). A GO term was considered specific if <200 genes were annotated with it. Same GO Annotation (filtered) “Same GO annotation” analysis was repeated, restricting analysis to gene pairs that could have had this characteristic a priori (i.e. eliminating pairs in which one or both genes lack an annotation for any specific GO term). Similar GO Annotation Pairs in which both genes are annotated with a pair of specific “similar GO” terms were collected from the Gene Ontology (S24). Similarity between two GO terms was

Page 9: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

9

objectively defined by the overlap in annotated genes, described below for the map between GO terms. Similar GO Annotation (filtered) “Similar GO annotation” analysis was repeated, restricting analysis to gene pairs that could have had this characteristic a priori (i.e. eliminating pairs in which one or both genes lacks an annotation for any specific similar GO terms). Same MIPS Protein Class Pairs of genes belonging to the same protein class (typically describing biochemical activity or structural role) were collected from the MIPS database (S13) in January 2003, excluding non-specific categories (i.e., those with names including the word “other” and those that contained more than 200 genes). Same Mutant Phenotype Pairs of genes annotated with the same mutant phenotype were collected from the MIPS database in January 2003, excluding non-specific phenotype categories, (e.g. categories with names including the word “other” and categories with more than 200 genes, or those at the least specific level of the hierarchy). Same Predicted Protein Complex Pairs were comprised of genes whose protein products were predicted to be in the same complex by a program called MCODE (S25). Finding Specific GO Attributes Frequently Connected by Genetic Interaction We considered 756 Gene Ontology (GO) (S26) attributes for which there are at least 10 and at most 80 annotated genes according to GO annotation by the Saccharomyces Genome Database (SGD), We used GO attribute association files as of Feb 19, 2003. Counts of annotated genes include upward-propagated associations. In other words, if a gene is associated with an attribute by SGD, then we propagate this association to all of the attribute's ancestors in the GO directed acyclic graph (DAG). A gene pair was said to be GO attribute-connected if both genes have the attribute, and genetically connected if a genetic interaction has been detected by SGA analysis. For each GO attribute examined, we tested the significance of association between genetic connection and GO attribute connection among the set of gene pairs that have been tested by SGA analysis (subject to the pre-processing steps above). Significance of the overlap between GO attribute-connected and genetically connected gene pairs was assessed by first calculating a P-value by a one-tailed Fisher’s Exact Test (which uses a cumulative hypergeometric distribution). We accounted for multiple hypothesis testing using a resampling approach. Specifically, we treated the Fisher’s Exact Test P-value as a test statistic and obtained the empirical distribution of this test statistic from randomly permuted assignment of genetic interaction to gene pairs. The reported P-value is calculated from this empirical distribution. More details on this approach have been described elsewhere (S27).

Page 10: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

10

Finding Pairs of GO Attributes that are Significantly Connected by Genetic Interaction We considered all 285,390 Gene Ontology (GO) (S26) pairs of the 756 GO attributes selected above. Here, a gene pair was said to connect a GO attribute pair (A, B) if one gene is annotated with attribute A, the other gene is annotated with attribute B, and if neither attribute A nor B are annotated to both genes. For each GO attribute pair, significance of association between genetic connection and GO attribute connection was assessed among SGA-tested gene pairs and corrected for multiple hypothesis testing as described above. Network View of Genetically Connected Functions Figure 1 of the manuscript was created using the Cytoscape network layout program (S10). For ease of visualization, the significance threshold of linked GO attributes was chosen to be (P < 0.002) as this created a manageable number of nodes and edges in the network. The layout was hand edited slightly to make the clusters more aesthetically pleasing (rounder), but the clustering was not affected. This was tested by determining the average path length from all the GO terms in one clustered group of functional categories to any GO term in another clustered group of functional categories. The average path lengths between combinations of the four clusters depicted in Figure 1 matched the network layout and were Green to red: 1.6; Blue to green: 2.2; Cyan to green: 2.5; Cyan to blue: 1.6; Cyan to red: 1.9; Blue to red: 1.4 where Green is DNA Synthesis, Recombination, Meiosis, DNA Repair; Red is Mitosis, Chromosome or Chromatin Structure; Cyan is Vesicular Transport and Blue is Cell Polarity, Cell Wall Maintenance, Cytokinesis. The categories of Transcription, Signaling and Other were ignored for this path length calculation because they were deemed unrelated to the main categories of interest above. Clustering GO Attributes for Display in a Matrix of Connected Functions We developed a simplified representation of the matrix of functions that are connected by genetic interaction (Fig. S9 and S10). In this matrix, we only considered the subset of GO attributes for which significant genetic interaction enrichment was determined above. For ease of visualization, we clustered GO attributes using the Fisher's Exact test P-value measuring the significance of overlap between the "function neighborhoods" as a proximity measure. Here, two GO attributes were defined as neighbors if gene pairs connecting these GO attributes interact genetically, significantly more often than by chance (see above). Clustering was accomplished by agglomerative hierarchical clustering with complete linkage. Clusters were not joined if the complete linkage proximity measure was above a threshold P-value corresponding to the case in which two GO attributes have exactly one GO attribute neighbor each, and this neighbor is the same for both nodes. Clusters and their component attributes are listed in Table S7. The matrix of connected functions and expanded views were produced using Mathematica (Wolfram Research). Defining Similar Pairs of GO Terms by Overlap in Assigned Gene Sets We defined whether two GO attributes, A and B, were similar in the sense of being assigned to overlapping sets of genes. This is equivalent to a test of association between

Page 11: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

11

two binary variables “Gene is annotated with GO attribute A?” and “Gene is annotated with GO attribute B?”. We used a Log Odds Ratio (LOD score (defined in (S27)) as a measure of the strength of association between these two variables, and Fisher’s Exact Test P-value as a measure of significance of association. We defined as similar any pair of GO attributes for which P<1.75E-7 (equivalent to an experiment-wise error rate of P<0.05 according to a conservative Bonferroni correction) and LOD>3. YMR299c: Construction of GFP-TUB1 Strains GFP-TUB1 was integrated in deletion mutants dyn1∆::kanR, arp1∆::kanR, ymr299c∆::kanR and BY4741 yeast strains individually by transforming the XbaI digested pAFS125 plasmid (S28). Ura+ transformants were selected and confirmed by fluorescence microscopy and PCR. YMR299c: Construction of YMR299c-3GFP Strain We constructed theYMR299c-3xGFP integration vector to integrate three tandem copies of GFP at the 3’ end of YMR299c locus as described in (S29). The final plasmid which contained a fragment of YMR299c fused with a triple GlyAla linker, triple GFP, and a nourseothricin resistant marker (S30) was linearize by AccI in the middle of the YMR299c fragment and transformed to BY4741. Transformants were grown on YPD plates containing nourseothricin (clonNAT) (100 ug/ml) and nourseothricin resistant strains were selected and confirmed for proper targeting by PCR. YMR299c: Fluorescence Microscopy

For nuclear migration analysis, cells were fixed with methanol/acetic acid (3:1) at room temperature for 30min, washed twice in PBS and then stained with DAPI (1ug/ml) for 30min, then further washed with PBS three times before mounting.

For analysis of microtubule phenotypes, cells expressing GFP-TUB1 were observed under a confocal fluorescence microscope with a 100x objective and using a live cell imaging system (UltraVIEWTM; PerkinElmer). Immunofluorescence of microtubules was performed as described (S31). Microtubules were stained with anti-α tubulin YOL1/34 at 1:100 dilution and goat anti-rat conjugated with rhodamine at a dilution of 1:200. Double-label immunofluorescence was carried out with rabbit anti-GFP at 1:100 dilution and goat anti-rabbit conjugated with fluorescein at a dilution of 1:100. Single images were collected under a conventional fluorescence microscope with a 100x objective and a CCD detector using Openlab (Improvision), and then processed using the Metamorph Imaging System (Universal Imaging Corp., West Chester, PA). The number of common neighbors between two genes in the SGA network correlates with a known protein-protein interaction between the protein products of those genes. While the predictive performance of this measure could be much improved (Fig. S5), the accuracy of the method was high when considering gene pairs with 50 common neighbors or more (Fig. S6). Given that very few gene pairs reached this threshold, we expect that the prediction performance will improve as the data set grows. Degree Distribution Analysis

Page 12: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

12

Since the synthetic genetic network examined here was derived from relatively few query genes tested against many array genes, the largest observable degree for array-only genes (genes in the array not also used as query genes) is much lower than that of query genes. Therefore, pooling the observed degrees of all genes would not be appropriate, and we chose to examine the degree distributions of array-only and query genes separately. The degree distribution of array-only genes fits a power-law distribution quite well, as shown in Fig. 4A in the manuscript. The degree distribution of query genes (Fig. S11) does not approximate a power-law distribution, nor does it approximate the expected degree distribution of any common network topology. Although there is little bias in the query degree distribution due to restricted observation (most potential partners of query genes were tested), this is a much smaller set than the array-only genes and furthermore was selected non-randomly so that its degree distribution may not be representative. A bias towards high-degree query genes might explain the much smaller fraction of nodes with low degree than expected in a scale-free graph. We should caution that the observed array gene distribution is also not free from bias. For instance, if an array gene interacts with at least one of the query genes, it is more likely to have a similar function and is therefore more likely to connect with other functionally-related query genes. Despite these caveats, our analysis provides support for a power-law distribution in synthetic genetic networks. Characteristic Path Length Analysis The characteristic path length of the SGA network is the average distance between two nodes (number of edges in the shortest path between the two nodes). We computed the characteristic path length of a random graph for two types of random graph: graphs with the same degree distribution, and Erdös-Rényi random graphs with the same degree distribution were constructed as previously described (S32). We generated 1000 instances of each type. Random graphs with the same degree distribution as the SGA network had characteristic path length 3.2 +/- 0.01. Erdös-Rényi random graphs SGA network had characteristic path length 3.6 +/- 0.01. From this we conclude that the characteristic path length of the SGA network is not significantly different than for a random graph, one of the two properties of a small-world network. Population Biology of Synthetic Genetic Interactions The frequency of a carrier with a mutant in a given query gene and mutant in a second locus giving a synthetic combination in gamete 1 = 10-3. The frequency of a carrier with a mutant in the same query gene and second locus giving a synthetic combination in gamete 2 = 10-3. Thus the probability of this synthetic combination in a diploid zygote formed from gametes in such a population is 10-3 X 10-3 = 10-6. We have taken the number of genes that, when mutant, give a synthetic combination with a given query gene to be 30. Thus, the probability of a synthetic combination with a given query gene is 10-6 x 30 = 3 x 10-5. The probability of no synthetic combination at this query locus = 1 - (3 x 10-5). The probability of no synthetic combination at any query locus = [1 - (3 x 10-5)]^L, where L is number of loci viable when null. For example, if L = 2500, then the probability of no synthetic combination at any query locus is exp (-(3 x 10-5)L) = 0.93. Thus, the probability of at least one synthetic combination = 0.07. For the cases in the paper where we take 10% and 50 % of L as the number of viable nulls that can

Page 13: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

13

participate in synthetic interactions, these number come to 0.75% and 3.7 % respectively, which have been rounded up to 0.8% and 4.0% in the text.

Page 14: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

14

0

0.2

0.4

0.6

0.8

1

-20 -15 -10 -5 0 5 10 15 20

Posi

tive/

All

t value Figure S1 The ratio of confirmed positives to all hits within the interval of the value of t-statistics for 10 screens, including BNI4, KRE1, APP1, CLB4, ARP1, JNM1, DYN1, CSM3, CTF18 and CHL1. Similar distributions can be obtained with regard to other calibration variables. Based on the knowledge of the confirmed positive rate, the possible number of false negative interactions can be estimated conservatively for hits that were not examined by the confirmation procedure. For example, among all 130 putative interactions within the interval 5~6 of the t-value, 28 positives and 30 negatives are scored. Of the other 72 putative interactions not examined, the chance for a positive score is estimated conservatively 28/130, i.e. about 16 true hits might be missed within the interval.

Page 15: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

15

0

50

100

150

200

250

300

350

400

450

0 2000 4000 6000 8000 10000

Num

ber o

f Pos

itive

Hits

Number of False Positive Hits

252

388, 35%

431, 41%

Confirmed positivet-value

Difference in growth rate

Figure S2 The detection of possible positive interactions with regard to the number of false positive interactions. From these 10 screens, 252 putative interactions confirmed positive out of the total 46418 interactions. The total number of possible positive interactions was estimated to be 388 and 431 for the calibration variables of t-value and difference in growth rate, respectively, as shown in Fig. S1, which suggests a false negative rate in the range of 35% to 41%.

Page 16: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

16

Sequence Alignment of Ymr299c * 20 * 40 * 60 * 80 Mouse : MAPVGVEKKLLLGPN----GPAVAAAGDLTSEEEEGQSLWSSILSEVSTRARSKLPSGKNILVFGEDGSGKTTLMTKLQ-GAEHG : 80 Rat : MAPVGVEKKLLLGPN----GPAVAAAGDLTSEEEEGQSLWSSILSEVSTRARSKLPSGKNILVFGEDGSGKTTLMTKLQ-GAEHG : 80 Human : MAPVGVEKKLLLGPN----GPAVAAAGDLTSEEEEGQSLWSSILSEVSTRARSKLPSGKNILVFGEDGSGKTTLMTKLQ-GAEHG : 80 Chicken : MAAVGRAGSFGSSSASGAANNASAELRAGGEED-DGQNLWSCILSEVSTRSRSKLPSGKSVLLLGEDGAGKTSLIGKIQ-GIEEY : 83 Frog : -MASGRTGSYSSPSSSFNAGYGQNQSGATASEDEDGQNLWSSILSEVSTRSRSKLPFGKNVLLLGEDGAGKTSLIGKLQ-GIEEY : 83 Anopheles : ---------------SQVHGLTTPTTAARKKDAEAKENLWSSILSEVQTQSNTKLPSNKSVLVLGDNASGKTTLIAKLQ-GVEDP : 69 FruitFly : ------------------------------------------------------------------------------------- : - Worm : --------MPPTAQPLEFDDTANAVLPVLYSSTDEEVGIWRELLASKKTNTNQ----GSTVIVLGDNRSGKSSLLSRLD-KSDRT : 72 Yeast : ---------------------------------MDNCNAWDKLLSQNESTINSTETATITAIIYSPSSKTLHQFINICFPEGSNS : 52 w ls g gk l * 100 * 120 * 140 * 160 * Mouse : KKGR-GLEYLYLSVHDEDRDD-----------------HTRCNVWILDGDLYHKGLLKFAVSAESLRETLVIFVADMSRPWTIME : 147 Rat : KKGR-GLEYLYLSVHDEDRDD-----------------HTRCNVWILDGDLYHKGLLKFAVSAESLRETLVIFVADMSRPWTIME : 147 Human : KKGR-GLEYLYLSVHDEDRDD-----------------HTRCNVWILDGDLYHKGLLKFAVSAESLPETLVIFVADMSRPWTVME : 147 Chicken : KKGR-GMEYLYLNVHDEDRDD-----------------QTRCNVRILDGDLYHKGLLKFAMEANSLKDTLIMLVVDMSRPWTAMD : 150 Frog : KKGR-GMEYLYINVHDDDRDD-----------------QTRCNVWILDGDLYHKGLLKFAMDPSSVRDTLIMLVVDMSRPWLALD : 150 Anopheles : KKGS-GLEYAYIDVRDEYRDD-----------------VTRLSVWILDGDPGHNNLLKFALNEQNFPHTLVILTLSMTTPWSWVD : 136 FruitFly : --------------------------------------MTRLGVWVLDGDPGHTNLLHYALNETNYAHTLVILTVSMTQPWGWLE : 47 Worm : VKPKSLLGYRVLHVQNDARDASYAYQLGTAGANLNPSELLQIPVWSLDGNAACASLLKHALP-ATPAEAIFILTASIDNPN-LIH : 155 Yeast : ILDTTLINYATIGWTNDLKEN----------------YSVDVYTLIRNTDDALDLLKPFLQEHSSKVRWLILLDWTLNDQKLWLN : 121 k y v d tr vw l1g1 h Llk a t6 6 6 pw 6 180 * 200 * 220 * 240 * Mouse : SLQKWASVLREHIDKMKIPPEEMRDLERKFMKEFQDYIEPEEGCQ-GSPQRRGPLTSGSDEDSVALPLGDNVLTHNLGIPVLVVC : 231 Rat : SLQKWASVLREHIDKMKIPPEEMRDLERKFMKDFQDYIEPEEGCQ-GSPQRRGPLTSGSDEDNVALPLGDNVLTHNLGIPVLVVC : 231 Human : SLQKWASVLREHIDKMKIPPEKMRELERKFVKDFQDYMEPEEGCQ-GSPQRRGPLTSGSDEENVALPLGDNVLTHNLGIPVLVVC : 231 Chicken : SLQKWASVVREHIDKLKIPPEEMKEMEQKLVRDFQEYVEPGEDFP-ASPQRRNTSLQEDKDDSVILPLGADTLTCNLGIPVVVVC : 234 Frog : SLQKWASVIREHVDKLKIPPEEMREMEERIVRHFQEYVEPGDELP-TSPQRRNTSSDE-CDDSVILPLADDTLTHNLGIPVVVVC : 233 Anopheles : QLQHWMKILDDHIAGLKIDPEEKQQCQARLTTEWQNYCETIDDLDPGSPIKRTNRLPSVDDELDALPLPEGVLTTNLGLDVVVVV : 221 FruitFly : QLNHWIKVLGQHIDSLQLDAKEKEAARQRLTTTWQSYCEVGDDLDPGSPVKRTMRNNSIDED-DLLPLTEDALITNLGLDIVVVV : 131 Worm : SLKRWANVCTEQAQKHFT-KEDLKAGRSQQEKMWQEYVDP------VQSQMSTSVVGSFADEHNLLPLDQGTLTENCGVTFMVVI : 233 Yeast : ELSYAFNKIKQLND---------------------------------------------DNEFSVWCLNSGEILN---------- : 151 L w h d e q y e sp r lpL 6t nlg vv 260 * 280 * 300 * 320 * 340 Mouse : TKCDAMSVLEKEHDYRDEHLDFIQAHLRRFCLQYGAALIYTSVKEEKN-----LDLLYKYIVHKTYG-FHFTIPALVVEKDAVFI : 310 Rat : TKCDAVSILEKEHDYRDEHLDFIQAHLRGFCLQYGAALIYTSVKEEKN-----LDLLYKYIVHKTYG-FHFTIPALVVEKDAVFI : 310 Human : TKCDAVSVLEKEHDYRDEHLDFIQSHLRRFCLQYGAALIYTSVKEEKN-----LDLLYKYIVHKTYG-FHFTTPALVVEKDAVFI : 310 Chicken : TKCDAISVLEKEHDYRDEHFDFIQSHIRRFCLQYGAALIYTSVKENKN-----IDLVYKYIVQKLYG-FPFNVPAVVVEKDAVFI : 313 Frog : TKCDAISILEKEHDYRDEHFDFIQSHIRKFCLQYGAALIYTSIKENKN-----IDIVYKYIVQQLYG-FQFKMPAVVVEKDAVFI : 312 Anopheles : TKTDYMTTLEKELDYRDEHFDFMQQWIRRFCLMYGASLFYTSVKEDKN-----CDLLYKYLTHRIYG-LPFRTPALVVEKDAVLI : 300 FruitFly : TKTDYMTTLEKEYEYRDEHFDFIQQWIRNFCLRHGTSLFYTSVKEDKN-----CDVLYKYLTHRIYG-LPFRTPALVVEKDAVLI : 210 Worm : TKSDLVLG----KEFTDAQFAKISIQLRKFCLSLGATLVFTSAKETKN-----IQLLQKYIVHRSFG-TAFTSAAQVIERESIFV : 308 Yeast : -------LQRHTTVWQSVHIDFILQTLRSFCYFNDSSLFYICEDHTEEKREEAQRLKYQELLKHFCEDRDMKDHIEMVTRSEILI : 229 tk d leke 5rdeh df6q 6R FCl ga L 5ts ke kn d6 yky6 g f pa 66e4da6 6 * 360 * 380 * 400 * 420 Mouse : PAGWDNEKKIAILHENFTTVKPEDAYEDFIVKPPVRKLVHDK--ELAAEDEQVFLMKQQSLLAKQP-ATPTRTSESPARGPSGSP : 392 Rat : PAGWDNEKKIAILHENFTTVKPEDAYEDFIVKPPVRKLVHDK--ELAAEDEQVFLMKQQ---------------ESPARGPSGSP : 378 Human : PAGWDNEKKIAILHENFTTVKPEDAYEDFIVKPPVRKLVHDK--ELAAEDEQVFLMKQQSLLAKQP-ATPTRASESPARGPSGSP : 392 Chicken : PAGWDNDKKIGILHENFQTLKAEDSFEDSIRKPPVRKFVHEK--EIVAEDDQVFLMKQQSQLAKQPPTAAGRPVDASPRVPGGSP : 396 Frog : PAGWDNDKKIGILHENFQTLKPEDTFEDVITKPPVRKFVHEK--EIVAEDDQVFLMKQQSQLAKQPPATAGR-QDASPRVPGGSP : 394 Anopheles : PAGWDNMKKISILYENMQSCKPDDYYNDIIAQPPSRKTVSNRESEIQTEDEQSFLARQQQLLQQ-------GQSPARGESPLRSQ : 378 FruitFly : PAGWDSLKKISILYENMHGVKAENPYTDIIKSPPTRKAVSNREAEVQTEDEQAFLARQQEILKQ-------GDQ-VRGESPLRSQ : 287 Worm : PAGWDGEKKIDIIRESIPDVDSALEPTRDKLRPVAKEQLIEA------EEDQAFLKKLMDILAT--------------------- : 366 Yeast : PKGCDSIGLIKTVDERFEPTEVK---------------------------EQHFLARYMDFIPT--------------------- : 266 PaGwD kkI i6 En k d i pp k e ed Q FL 4qq p s * 440 * 460 * 480 * 500 * Mouse : RTQGRGGPASVPSASPGTS-VKKPDPNIKNNAAS-EGVLASFFNSLLSKKTGSPGSPSAGG--------------VQSTAKKS-- : 459 Rat : RTQGRGGPASVPSASPGTS-VKKPDPNIKNNAAS-EGVLASFFNSLLSKKTGSPGSPSAGG--------------VQSTAKKSGT : 447 Human : RTQGRGGPASVPSSSPGTS-VKKPDPNIKNNAAS-EGVLASFFNSLLSKKTGSPGSPGAGG--------------VQSTAKKS-- : 459 Chicken : RTPNRSVTSNVASVTPIPAGSKKIDPNMKAGATS-EGVLANFFNSLLSKKTGSPGGPGGVGGSPGGGSAGGTGSNLPPSAKKS-- : 478 Frog : RTPSRSGSTNVASVSPVPAGTKKIDPNMKAGTTS-EGVLANFFNSLLSKKTGSPG-AGGTG-IPAGNSTG---NSLPASAKKT-- : 471 Anopheles : PNNGTKSTQRTPVAAGAQGSPKKVDGKLTPGTQSGEGVLANFFNSLLHKNASSS----PVSSLSPRVSV------LNGTG-EPVS : 452 FruitFly : GVGSNKSGPRTPGTTG-QSSPKKIDPKLTPATPGAEGVLANFFNSLLHKKSGSPGTGGPGGAGNPAGPG------RTANGTDAVM : 365 Worm : ---------STTTAAPKPR-------TMQEEPTDKDSPLANFFSNLLNKDKPSK---------------------VSSPSTVS-- : 412 Yeast : ------------------------IDKIREDRKTTSGIDLDKLYPLEVFK----------------------------------- : 292 kk d 6 eg la ffnsLl kk s 520 * 540 * 560 Mouse : -----------------GQKTVLSNVQEELDRMTRKPDSMVTN---SSTENEA- : 492 Rat : EGEPQSFRSLTEQCCQTGQKTVLSNVQEELDRMTRKPDSMVTN---SSTENEA- : 497 Human : -----------------GQKTVLSNVQEELDRMTRKPDSMVTN---SSTENEA- : 492 Chicken : -----------------GQKPVLTDVQAELDRISRKPEMVSPTSPTSPTEGEAS : 515 Frog : -----------------GQKPVLTDVQAELERISRKPDIVSPTTPTSPTENDTS : 508 Anopheles : AS---------------DKLSMRTDAALELDRLAR---SVKKDLDISATQSDC- : 487 FruitFly : TP---------------EKLAVRTDAAAELDRLSR---SVKKEIDMS--QSEC- : 398 Worm : ------------------QPMDAAATQAQLDRLLKSAQSPKPQ----PRDSDA- : 443 Yeast : -----------------------VNIQEELGKMFAKYRENSRI----------- : 312 q 2Ld46 s

Figure S3. Multiple sequence alignment of Ymr299c showing conservation across eukaryotes for the dynein light intermediate chain protein. Alignment was constructed using ClustalX 1.83 and subsequently colored using GeneDoc. Numbers above the alignment indicate the sequence position. Letters under the alignment show the consensus motif, with lower and upper case letters showing medium and high levels of conservation, respectively, and numbers indicating conserved similar residues (i.e. 1=DN similarity group, 2=EQ, 3=ST, 4=KR, 5= FYW, 6=LIVM). Zoom in (250%) see more detail. The following protein database records from NCBI’s Entrez system were used in the alignment:

Page 17: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

17

Mouse (gi|23633509) similar to Dynein light intermediate chain 2 Rat (gi|13591938) dynein light intermediate chain Human (gi|5453634) dynein, cytoplasmic, light intermediate polypeptide 2 Chicken (gi|2494217) Dynein light chain A Frog (gi|28280005) similar to cytoplasmic dynein light-intermediate chain Anopheles Anopheles gambiae (gi|31204625) FruitFly (gi|24641230) Worm (gi|25151901) cytoplasmic Dynein Light chain, Intermediate type Yeast: (gi|6323957) Ymr299cp Localization of Ymr299c and Microtubules

Figure S4.

A. Immunofluorescence of both microtubules and Ymr299c showed that Ymr299c localized to motile cortical dots and colocalized to the tips of cytoplasmic microtubules. Microtubules were stained with anti-α tubulin YO L1/34 at 1:100 dilution and goat anti-rat conjugated with rhodamine at a dilution of 1:200; and rabbit anti-GFP at1:100 dilution and goat anti-rabbit conjugated with fluorescein at a dilution of 1:100.

B. The percentage of nuclear positioning defects in cells. Wild-type and mutant strains ymr299c∆, dyn1∆, and arp1∆ were fixed, stained with DAPI, and then scored for nuclear position. The position and phenotype of nuclear DNA was visualized by DAPI staining, and scored for abnormal morphology corresponding to the phenotypes schematically depicted. The first column shows the percentage of cells with the nucleus failed to position at the bud neck; the second column shows the percentage of cells with anaphase occurring in the mother cell; and the third column shows the percentage of cells with both nuclei in the mother cell. The total percentage of defects is the sum of percentage of cells with abnormal phenotypes. n = 500 cells for each strain.

Page 18: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

18

Protein-Protein Interaction Prediction Performance from SGA Common Neighbor Gene Pairs

0

10

20

30

40

50

60

70

80

90

100

0 5 10 15 20 25 30 35 40 45

Sensitivity (%)

Acc

urac

y (%

)

AllYeast(SpokeMS) AllYeast(MatrixMS)

Gene pairs with 50 or morecommon neighbors

Gene pairs with 2 or morecommon neighbors

Figure S5. Prediction Performance of Common Neighbor Protein-Protein Interaction Measure Accuracy (sometimes called specificity) is the ratio of true protein-protein interactions to total predicted interactions (if a predicted interaction occurs between genes with many common neighbors). Sensitivity is the ratio of true protein-protein interactions to the total number of protein interactions that could be predicted, in this case the number of protein interactions among any of the 649 genes in the above 1 common neighbor network (443 possible protein interactions). AllYeast(SpokeMS) is a set of 15,143 protein-protein interactions including large-scale mass spectrometry study copurifications represented using the spoke model (bait connected to hits). AllYeast(MatrixMS) contains 52,345 protein-protein interactions including the mass spectrometry copurifications represented using the matrix model (all copurified proteins interconnected) (S21).

Page 19: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

19

SGA gene pairs with many common neighbors tend to be protein interactions

111317171717171718181921222526

2933

36

3944

50

58

64

0

200

400

600

800

1000

1200

10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 40 50

Common Neighbor Threshold

Num

ber o

f Gen

e Pa

irs

0

10

20

30

40

50

60

70

80

90

100

Acc

urac

y (%

)

Protein interactions Accuracy

1115 Gene Pairs With 10 or MoreCommon Neighbors. 64 of These AreProtein-Protein Interactions

Figure S6. Protein-Protein Interaction Prediction Accuracy Grows with the Number of Neighbors Shared by SGA Gene Pairs. The number of gene pairs with at least the given number of common neighbors (common neighbor threshold) is shown (Dark Purple + Light Purple) along with the number of known protein-protein interactions that overlap (Dark Purple). The number of gene pairs at a common neighbor threshold that don’t overlap with known protein-protein interactions is shown as well (Light Purple). The accuracy of the protein-protein interaction measure is superimposed (Blue line).

Page 20: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

20

Figure S7. Examples of the spot assay version of random spore analysis: MATa meiotic progeny derived from sporulation of heterozygous diploids, MATa/α dcc1∆::natR/+ bim1∆::kanR/+ or MATa/α dcc1∆::natR/+ bni1∆::kanR/+ , spotted on to medium [SD/(MSG) – His/Arg + canavanine] containing the antibiotics as indicated. The cultures were incubated at 30oC for ~2 days. Cell growth under the three conditions was compared and scored. The MATa dcc1∆::natR bim1∆::kanR double mutant was scored as having a synthetic genetic interaction (Yes), whereas the MATa dcc1∆::natR bni1∆::kanR double mutant was not (No).

Figure S8. The complexity of genetic interactions with the gene CFTR, mutations in this gene cause the cystic fibrosis phenotype (S34).

Page 21: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

21

Figure S9. A matrix of connections between gene functions based on synthetic genetic interaction. Colored cells in this matrix represent pairs of GO attributes that are associated with genetic interactions more than would be expected by chance (P < 0.05); we say that the attributes in such pairs are “genetically connected”. P-values have been corrected for multiple hypothesis testing by resampling (S27), so that it would be unlikely (1 chance in 20) to find any filled cells in this table if synthetic interaction and GO annotation were unrelated. Each grey cell (always along the diagonal) represents a GO attribute for which genetic interactions between genes each with that attribute are surprisingly abundant (P<.05 with multiple hypothesis correction). Each black cell indicates a pair of genetically-connected GO attributes; each blue cell indicates a pair of genetically-connected attributes that are also similar in the sense that there is significant overlap in the sets of genes associated with each attribute (described further below). We define the “neighbor set” of a GO attribute as the set of GO attributes that are “genetically connected” to it; GO attributes were clustered according to the degree of overlap of their neighbor sets (cluster numbers are shown along the axes). Clusters and their component attributes are listed in Table S7.

Page 22: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

22

Figure S10. A subregion of the matrix of connections between gene functions based on synthetic genetic interaction. The coloring of the cells is as described for Fig. S9. GO attribute names are colored according to Molecular Function (blue), Biological Process (green), and Cellular Component (red) branches of the Gene Ontology. Clusters and their component attributes are listed in Table S7.

Page 23: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

23

Degree Distribution of Query Genes

0

1

2

3

4

5

6

7

8

0 20 40 60 80 100 120 140 160 180

Degree

Gen

e C

ount

Figure S11. The degree distribution of query genes.

Page 24: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

24

Table S1. A table summarizing all the synthetic lethal/fitness interactions. [see pages 37 to 111] Table S2 summarizes the average number of interactions/protein in various protein interaction datasets Dataset (S21) Average number of interactions/protein TAP (spoke) 7.5 HMS-PCI (spoke) 8.5 TAP and HMS-PCI combination (spoke) 8.0 TAP and HMS-PCI combination (spoke) reduced to only cases where MS bait matched an SGA query (34 occurrences)*

7.4

Ito and Uetz Y2H screens reduced to only cases where MS bait matched an SGA query

1.5

All known yeast protein-protein interactions (SGA queries only)

6.8

Estimated yeast interactome size (S33) 3-5 *Average number of non-redundant SGA interactions for these 34 queries that matched either a bait in TAP or HMS-PCI: 31.7 Table S3. Association between synthetic genetic interaction (S) and other gene- or protein-pair characteristics. Among gene pairs tested by SGA, columns 2-5 show the numbers of gene pairs with both S and a given query characteristic C; the number with only S; with only C; and with neither. The remaining columns show “P(C|S),” the probability that a gene pair possesses the query characteristic, given that it is S; “Odds,” the ratio of P(C|S) to P(C|not S); “P(S|C),” the probability that a gene pair is S, given that it possesses the query characteristic; and “P-value,” the significance of overlap between S and C, as computed by Fisher's Exact Test. Significance of association (indicated by shading) required a P-value of < 0.002, established by the conservative Dunn-Sidak correction to yield an experiment-wise error rate < 0.05.

Query Characteristic S+C S

only C

only Neither P(C|S) Odds P(S|C) P-value Similar GO annotation 813 2247 26166 698133 0.27 7 0.03 <2E-322 Same MIPS mutant phenotype 456 2604 9311 714988 0.15 12 0.05 9E-316 Same GO annotation 418 2642 8153 716146 0.14 12 0.05 5E-296 Similar GO annotation (filtered) 813 1519 26166 296196 0.35 4 0.03 1E-286 Same GO annotation (filtered) 418 1914 8153 314209 0.18 7 0.05 2E-211 Same subcellular localization 125 2935 3488 720811 0.04 8 0.03 2E-70 Physical interaction: same MIPS complex 88 2972 1439 722860 0.03 14 0.06 4E-68 Physical interaction 104 2956 2579 721720 0.03 10 0.04 2E-63 Physical interaction: same MIPS complex (no subcomplexes) 24 3036 162 724137 8E-03 35 0.13 5E-28 Sequence homology (BLAST E-value < 1E-3) 47 3013 1771 722528 0.02 6 0.03 4E-22 Same predicted complex (using MCODE) 28 3032 904 723395 9E-03 7 0.03 2E-15 Correlated mRNA expression (Cho, CC > 0.7) 59 3001 6169 718130 0.02 2 9E-03 2E-08 Physical interaction: APMS (TAP or HMS-PCI) 17 3043 1029 723270 6E-03 4 0.02 4E-06 Physical interaction: HMS-PCI 11 3049 697 723602 4E-03 4 0.02 3E-04 mRNA coexpression 74 2986 11669 712630 0.02 1.5 6E-03 6E-04 Physical interaction: TAP 6 3054 345 723954 2E-03 4 0.02 4E-03 Physical interaction: Y2H U APMS "spoke" 5 3055 290 724009 2E-03 4 0.02 9E-03 Physcial interaction: Y2H: Ito3+, Uetz 2 3058 61 724238 7E-04 8 0.03 0.03 Common upstream regulator (P < 0.001) 41 3019 7118 717181 0.01 1.4 6E-03 0.03 Physical interaction: Y2H Ito3+ 1 3059 21 724278 3E-04 11 0.05 0.09 Physical interaction: Y2H Uetz 1 3059 47 724252 3E-04 5 0.02 0.18

Page 25: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

25

Correlated mRNA expr (Rosetta, CC < -0.7) 3 3057 513 723786 1E-03 1.4 6E-03 0.37 Correlated mRNA expr (Rosetta, CC > 0.7) 2 3058 694 723605 7E-04 0.7 3E-03 0.79 Correlated mRNA expr (Cho, CC < -0.7) 4 3056 2612 721687 1E-03 0.4 2E-03 1 Chromosomal distance < 7kb 0 3060 1033 723266 0 0 0 1 Gene cooccurence 0 3060 6 724293 0 0 0 1 Gene fusion 0 3060 3 724296 0 0 0 1 Phys intxn (Uetz, Ito3) mutual corr coefficient > 0 0 3060 234 724065 0 0 0 1 Phys intxn (Uetz, Ito3) mutual corr coefficient > 3 0 3060 226 724073 0 0 0 1 Same gene neighborhood 0 3060 62 724237 0 0 0 1

Table S4. A table of genetic interactions identified for gene pairs tested in the neighborhood density analysis. [see pages 112 to 189] Table S5. A table summarizing the genetic interactions identified in the BNI1 BIM1 triple mutant screen. The “Genetic Interaction – Gene Name” column indicates the gene identified as an interactor in the BNI1 BIM1 triple mutant screen. The “Genetic Interaction – Systematic Name” column indicates the systematic (ORF) name that corresponds to the interactor gene. The “BNI1” column contains the double-mutant phenotype between bni1∆::URA3 and xxx∆::kanR as confirmed by tetrad analysis. The “BIM1” column contains the double-mutant phenotype between bim1∆::natR and xxx∆::kanR as confirmed by tetrad analysis. The “BNI1 BIM1” column contains the triple-mutant phenotype between bni1∆::URA3 bim1∆::natR and xxx∆::kanR as confirmed by tetrad analysis. “SS” refers to a synthetic sick interaction; “SL” refers to a synthetic lethal interaction; “No” refers to an interaction that was tested but showed no SS or SL phenotype; “N/D” refers to test not done.

Genetic Interaction - Gene Name

Genetic Interaction - Systematic Name BNI1 BIM1 BNI1 BIM1

IKI3 YLR384C SS SS SL INO2 YDR123C No No SS RPN10 YHR200W No No SS CHS7 YHR142W SS No SL BEM1 YBR200W SL SL N/D CLA4 YNL298W SL SL N/D NBP2 YDR162C SS SS No SAC3 YDR159W SS SL N/D YKE2 YLR200W SS SL N/D SMI1 YGR229C SL SL N/D CYK3 YDL117W SS SS No SHS1 YDL225W SL SS N/D FAB1 YFR019W SL SL N/D ASE1 YOR058C SL SL N/D DYN1 YKR054C SL SL N/D DYN2 YDR424C SS SL N/D PAC11 YDR488C SL SL N/D ARP1 YHR129C SL SL N/D JNM1 YMR294W SL SL N/D NIP100 YPL174C SL SL N/D NUM1 YDR150W SL SL N/D PAC1 YOR269W SL SL N/D ELP2 YGR200C SL SL N/D ELP3 YPL086C SS SS No ELP4 YPL101W SL SL N/D ELP6 YMR312W SL SL N/D KRE24 YPL102C SL SL N/D MTM1 YLR190W SS SS No UBA4 YHR111W SS SS No VID22 YLR373C SL SL N/D YDR149C SL SL N/D

Page 26: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

26

YGR228W SL SL N/D YLL049W SS SL N/D YMR299C SL SL N/D YPT6 YLR262C SS SS No PCL1 YNL289W SS No No SWE1 YJL187C SS No No SWI4 YER111C SL No No BEM2 YER155C SL No No BEM4 YPL161C SL No No BUD6 YLR319C SS No No ELM1 YKL048C SS No No GIN4 YDR507C SL No No NAP1 YKR048C SS No No SLA1 YBL007C SS No No ATS1 YAL020C SL No No CHS5 YLR330W SS No No BCK1 YJL095W SL No No CHS3 YBR023C SL No No SKT5 YBL061C SS No No SLT2 YHR030C SL No No BNI4 YNL233W SL No No BNR1 YIL159W SL No No PIN4 YBL051C SL No No TIP41 YPR040W SS No No BBC1 YJL020C SS No No TUS1 YLR425W SL No No YBL062W SS No No YKR047W SS No No YNL119W SS No No DRS2 YAL026C SL No No SNC2 YOR327C SL No No VPS28 YPL065W SL No No MDM20 YOL076W SS N/D N/D BCK1 YJL095W SL N/D N/D ERG2 YMR202W SS N/D N/D ERG3 YLR056W SS N/D N/D VPS67 YKR020W SS N/D N/D YBL062W YBL062W SS N/D N/D YOR322C YOR322C SS N/D N/D YNL201C No SS No ARP6 YLR085C No SS No TUB3 YML124C No SL No GIM3 YNL153C No SL No GIM4 YEL003W No SL No GIM5 YML094W No SL No PAC10 YGR078C No SL No CIN1 YOR349W No SL No CHL1 YPL008W No SL No CHL4 YDR254W No SL No IML3 YBR107C No SL No CTF3 YLR381W No SL No CTF19 YPL018W No SL No MCM16 YPR046W No SL No MCM21 YDR318W No SL No MCM22 YJR135C No SL No NKP1 YDR383C No SS No NKP2 YLR315W No SS No CTF4 YPR135W No SL No CTF8 YHR191C No SL No CTF18 YMR078C N/D SL N/D DCC1 YCL016C No SL No HTZ1 YOL012C No SL No SAP30 YMR263W No SL No SLK19 YOR195W No SL No MMS1 YPR164W No SL No MRC1 YCL060C No SL No

Page 27: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

27

MRE11 YMR224C No SL No RAD52 YML032C No SS No RAD54 YGL163C No SL No RAD61 YDR014W N/D SL N/D TOF1 YNL273W Linked SL No DEP1 YAL013W No SL No INP52 YNL106C No SL No CSM3 YMR048W No SL No MCK1 YNL307C No SL No BIK1 YCL029C No SL No CIN8 YEL061C No SS No KIP2 YPL155C No SL No KIP3 YGL216W No SL No MAD1 YGL086W No SL No MAD2 YJL030W No SL No MAD3 YJL013C No SL No BUB1 YGR188C No SL No BUB2 YMR055C No SL No BUB3 YOR026W No SL No BFA1 YJR053W No SL No MSN5 YDR335W No SS No PHO23 YNL097C No SL No KEM1 YGL173C No SL No PPZ1 YML016C No SL No AOR1 YBR231C No SL No IPK1 YDR315C N/D SL N/D LSM1 YJL124C N/D SL N/D IES2 YNL215W No SS No KTI12 YKL110C No SS No RTT103 YDR289C No SS No RXT2 YBR095C No SL No VID21 YDR359C No SL No YDR360W No SL No YGL211W No SS No YGL217C No SL No YML094C-A No SL No YNL136W No SS No YNL170W No SL No YPL017C No SL No BRE5 YNR051C N/D SL N/D VAC14 YLR386W No SL No YTA7 YGR270W No SL No

Table S6. A table summarizing the genetic interactions identified in the BNI1 KRE1 triple mutant screen. The “Genetic Interaction – Gene Name” column indicates the gene identified as an interactor in the BNI1 KRE1 triple mutant screen. The “Genetic Interaction – Systematic Name” column indicates the systematic (ORF) name that corresponds to the interactor gene. The “BNI1” column contains the double-mutant phenotype between bni1∆::URA3 and xxx∆::kanR as confirmed by tetrad analysis. The “KRE1” column contains the double-mutant phenotype between kre1∆::natR and xxx∆::kanR as confirmed by tetrad analysis. The “BNI1 KRE1” column contains the triple-mutant phenotype between bni1∆::URA3 kre1∆::natR and xxx∆::kanR as confirmed by tetrad analysis. “SS” refers to a synthetic sick interaction; “SL” refers to a synthetic lethal interaction; “No” refers to an interaction that was tested but showed no SS or SL phenotype ; “N/D” refers to test not done.

Genetic Interaction - Gene Name

Genetic Interaction - Systematic Name BNI1 KRE1 BNI1 KRE1

SWI4 YER111C No No SS BUD19 YJL188C No No SS CAP1 YKL007W No No SL

Page 28: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

28

CAP2 YIL034C No No SL CHS6 YJL099W No No SS ALG5 YPL227C No No SS ALG6 YOR002W No No SS ALG8 YOR067C No No SS MNN2 YBR015C No No SS YPT31 YER031C No No SS SYS1 YJL004C No No SL ARL1 YBR164C No No SL ARL3 YPL051W No No SS APM1 YPL259C No No SS AGE2 YIL044C No No SS GTR1 YML121W No No SS ELM1 YKL048C slightly SS No SS MMR1 YLR190W No SS SL OST3 YOR085W No slightly SS SS INP53 YOR109W No slightly SS SS COG5 YNL051W No slightly SS SS COG7 YGL005C No slightly SS SS COG8 YML071C No slightly SS SS VAC7 YNL054W No SS SL ERG2 YMR202W SS SS SL ERG3 YLR056W SS SS SL ERG5 YMR015C No slightly SS SS YFR043C No SS SL YGR228W No SS SL BEM2 YER155C SL SS N/D CHS3 YBR023C SS SS No SKT5 YBL061C SS SS No CHS5 YLR330W SS SS No SLT2 YHR030C SL SL N/D BCK1 YJL095W SL SS N/D SMI1 YGR229C SL SL N/D DRS2 YAL026C SL SS N/D FAB1 YFR019W SL SL N/D NBP2 YDR162C SS SS No VPS67 YKR020W SS SS No YBL062W SS SS No BBC1 YJL020C SS No No BEM1 YBR200W SL No No BEM4 YPL161C SS No No BNI4 YNL233W SS No No BNR1 YIL159W SL No No BUD6 YLR319C SS No No CHS7 YHR142W SS No No CLA4 YNL298W SL No No ASE1 YOR058C SL No No NUM1 YDR150W SL No No PAC1 YOR269W SL No No DYN1 YKR054C SL No No PAC11 YDR488C SL No No YMR299C SL No No ARP1 YHR129C SL No No JNM1 YMR294W SL No No NIP100 YPL174C SL No No PCL1 YNL289W SS No No SWE1 YJL187C SS No No TUS1 YLR425W SS No No YKE2 YLR200W SS No No YDR149C SL No No YOR322C SS No No ATS1 YAL020C SL N/D N/D CYK3 YDL117W SS N/D N/D DYN2 YDR424C SS N/D N/D ELP2 YGR200C SL N/D N/D ELP3 YPL086C SS N/D N/D

Page 29: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

29

ELP4 YPL101W SL N/D N/D ELP6 YMR312W SL N/D N/D GIN4 YDR507C SL N/D N/D KRE24 YPL102C SL N/D N/D MDM20 YOL076W SS N/D N/D MTM1 YLR190W SS N/D N/D NAP1 YKR048C SS N/D N/D PIN4 YBL051C SL N/D N/D SAC3 YDR159W SS N/D N/D SHS1 YDL225W SL N/D N/D SLA1 YBL007C SS N/D N/D SNC2 YOR327C SL N/D N/D TIP41 YPR040W SS N/D N/D UBA4 YHR111W SS N/D N/D VID22 YLR373C SL N/D N/D VPS28 YPL065W SL N/D N/D YKR047W YKR047W SS N/D N/D YLL049W YLL049W SS N/D N/D YNL119W YNL119W SS N/D N/D YPT6 YLR262C SS N/D N/D CNB1 YKL190W No SS No CNE1 YAL058W No SL No CWH41 YGL027C No SL No DFG5 YMR238W No SL No ERD1 YDR414C No SL No GAS1 YMR307W No SL No GUP1 YGL084C No SL No HOC1 YJR075W No SL No HUR1 YGL168W No SL No ILM1 YJR118C No SL No KEX1 YGL203C No SL No KEX2 YNL238W No SL No KRE11 YGR166W No SL No MNN11 YJL183W No SL No PER1 YCR044C No SS No RHK1 YBL082C No SS No ROT2 YBR229C No SL No SAC7 YDR389W No SL No STE24 YJR117W No SS No YUR1 YJL139C No SS No YAL053W No SL No YAL056C-A No SL No YBL083C No SS No COG6 YNL041C No SS No GOS1 YHL031C No SL No PMR1 YGL167C No SL No SEC66 YBR171W No SS No MNN10 YDR245W No SL No PMT2 YAL023C No SL No YKL077W No SS No BUD14 YAR014C N/D SS N/D ERG28 YER044C N/D SL N/D KRE20 YAL058C-A N/D SL N/D KRE9 YJL174W N/D SL N/D OPI3 YJR073C N/D SS N/D PTC1 YDL006W N/D SS N/D SAC6 YDR129C N/D SS N/D SHE4 YOR035C N/D SL N/D TOM37 YMR060C N/D SS N/D MNN11 YJL183W N/D SL N/D

Table S7. A table of GO attribute clusters identified in Fig. S9 and their component attributes. 0 0015630 C microtubule cytoskeleton

Page 30: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

30

0005874 C microtubule 0003774 F motor 0008017 F microtubule binding 0000090 P mitotic anaphase 0005815 C microtubule organizing center 0005816 C spindle pole body 0030615 C spindle pole 0005819 C spindle 0005876 C spindle microtubule 0000071 P mitotic spindle assembly (sensu Saccharomyces) 0030472 P mitotic spindle assembly (sensu Fungi) 0000072 P M-phase specific microtubule process 0007051 P spindle assembly 0007052 P mitotic spindle assembly 0007059 P chromosome segregation 0005699 C kinetochore 0005698 C centromere 0015631 F tubulin binding 0007020 P microtubule nucleation 0008092 F cytoskeletal protein binding 1 0016288 P cytokinesis 0000142 C contractile ring (sensu Saccharomyces) 0005826 C contractile ring 0030480 C contractile ring (sensu Fungi) 0006893 P Golgi to plasma membrane transport 0006030 P chitin metabolism 0042546 P cell wall biosynthesis 0009272 P cell wall biosynthesis (sensu Fungi) 0005976 P polysaccharide metabolism 0016051 P carbohydrate biosynthesis 0000271 P polysaccharide biosynthesis 0006887 P exocytosis 0009581 P perception of external stimulus 0009582 P perception of abiotic stimulus 0009593 P perception of chemical substance 0000749 P response to pheromone during conjugation with cellular fusion 0019236 P response to pheromone 0007600 P sensory perception 0007606 P chemosensory perception 2 0007534 P gene conversion at MAT locus 0007533 P mating-type switching/recombination 0007530 P sex determination 0007531 P mating-type determination 0000723 P telomere maintenance 0006311 P meiotic gene conversion 0006974 P response to DNA damage 0007127 P meiosis I 0007128 P meiotic prophase I 0007131 P meiotic recombination 0007143 P female meiosis 0007144 P female meiosis I 0000077 P DNA damage checkpoint 0006302 P double-strand break repair 0006312 P mitotic recombination 0000724 P double-strand break repair via homologous recombination 0000725 P recombinational repair 0045003 P double-strand break repair via synthesis-dependent strand annealing 3 0006301 P post-replication repair 0006271 P DNA strand elongation

Page 31: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

31

0006272 P leading strand elongation 0006273 P lagging strand elongation 0045005 P maintenance of fidelity during DNA dependent DNA replication 0003887 F DNA-directed DNA polymerase 0006298 P mismatch repair 0006313 P DNA transposition 0006289 P nucleotide-excision repair 0016779 F nucleotidyltransferase 0004386 F helicase 0003678 F DNA helicase 0000726 P non-recombinational repair 0004527 F exonuclease 0004520 F endodeoxyribonuclease 0004536 F deoxyribonuclease 0004519 F endonuclease 4 0004702 F receptor signaling protein serine/threonine kinase 0006970 P response to osmotic stress 0006897 P endocytosis 0030479 C actin cortical patch (sensu Fungi) 0005857 C actin cortical patch (sensu Saccharomyces) 0007121 P polar budding 0030036 P actin cytoskeleton organization and biogenesis 0007015 P actin filament organization 0006403 P RNA localization 0007117 P bud growth 0000143 C actin cap (sensu Saccharomyces) 0030478 C actin cap (sensu Fungi) 0007118 P apical bud growth 0003779 F actin binding 0005200 F structural constituent of cytoskeleton 5 0007102 P spindle pole body and microtubule cycle (sensu Saccharomyces) 0030471 P spindle pole body and microtubule cycle (sensu Fungi) 0000065 P nuclear migration (sensu Saccharomyces) 0030473 P nuclear migration (sensu Fungi) 0007097 P nuclear migration 0000075 P cell cycle checkpoint 0007088 P regulation of mitosis 0007093 P mitotic checkpoint 0007094 P mitotic spindle checkpoint 0005657 C replication fork 0007062 P sister chromatid cohesion 0030261 P chromosome condensation 0005708 C mitotic chromosome 6 0008483 F transaminase 0008415 F acyltransferase 0006612 P protein-membrane targeting 0016746 F transferase, transferring acyl groups 0016747 F transferase, transferring groups other than amino-acyl groups 0040020 P regulation of meiosis 0016769 F transferase, transferring nitrogenous groups 0016407 F acetyltransferase 0004540 F ribonuclease 0004402 F histone acetyltransferase 7 0016570 P histone modification 0016569 P covalent chromatin modification 0005096 F GTPase activator 0006613 P co-translational membrane targeting

Page 32: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

32

0006614 P SRP-dependent, co-translational membrane targeting 0006616 P SRP-dependent, co-translational membrane targeting, translocation 0006476 P protein amino acid deacetylation 0016485 P protein processing 0005643 C nuclear pore 8 0005795 C Golgi stack 0000030 F mannosyltransferase 0006486 P protein amino acid glycosylation 0009100 P glycoprotein metabolism 0009101 P glycoprotein biosynthesis 0016758 F transferase, transferring hexosyl groups 0006888 P ER to Golgi transport 0006487 P N-linked glycosylation 9 0007119 P isotropic bud growth 0007125 P invasive growth 0007149 P colony morphology 0006348 P chromatin silencing at telomere 0000118 C histone deacetylase complex 0004407 F histone deacetylase 0007264 P small GTPase mediated signal transduction 0007266 P Rho protein signal transduction 10 0007034 P vacuolar transport 0007035 P vacuolar acidification 0006896 P Golgi to vacuole transport 0016023 C cytoplasmic vesicle 0016471 C hydrogen-translocating V-type ATPase complex 0030117 C membrane coat 0006892 P post Golgi transport 0005977 P glycogen metabolism 11 0005933 C bud 0005935 C bud neck 0005934 C bud tip 0008047 F enzyme activator 0007124 P pseudohyphal growth 0040007 P growth 0007150 P growth pattern 0005057 F receptor signaling protein 12 0003767 F co-chaperone 0000079 P regulation of CDK activity 0016538 F cyclin-dependent protein kinase, regulator 0019887 F protein kinase regulator 0003754 F chaperone 0000011 P vacuole inheritance 0004693 F cyclin-dependent protein kinase 13 0007031 P peroxisome organization and biogenesis 0004298 F threonine endopeptidase 0004299 F proteasome endopeptidase 0005837 C 26S proteasome 0005839 C 20S core proteasome 0008054 P cyclin catabolism 14 0006906 P non-selective vesicle fusion

Page 33: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

33

0005478 F intracellular transporter 0005484 F SNAP receptor 0005485 F v-SNARE 0016194 P non-selective vesicle exocytosis 0005768 C endosome 15 0042244 P spore wall assembly 0006112 P energy reserve metabolism 0030476 P spore wall assembly (sensu Fungi) 0007152 P spore wall assembly (sensu Saccharomyces) 0016052 P carbohydrate catabolism 16 0007030 P Golgi organization and biogenesis 0008080 F N-acetyltransferase 0000042 P protein-Golgi targeting 0016410 F N-acyltransferase 0045053 P Golgi retention 17 0007032 P endosome organization and biogenesis 0016197 P endosome transport 0006623 P protein-vacuolar targeting 0003925 F small monomeric GTPase 0005625 C soluble fraction 18 0016440 P transcriptional gene silencing 0016458 P gene silencing 0030466 P chromatin silencing at silent mating type cassettes (sensu Fungi) 0006347 P chromatin silencing at HML and HMR (sensu Saccharomyces) 0006342 P chromatin silencing 19 0016896 F exoribonuclease, producing 5'-phosphomonoesters 0004532 F exoribonuclease 0005635 C nuclear membrane 0006944 P membrane fusion 20 0000070 P mitotic chromosome segregation 0005711 C meiotic chromosome 0006261 P DNA dependent DNA replication 0006270 P DNA replication initiation 21 0005525 F GTP binding 0003924 F GTPase 0019001 F guanyl nucleotide binding 22 0008134 F transcription factor binding 0000082 P G1/S transition of mitotic cell cycle 0003712 F transcription cofactor 23 0016944 F Pol II transcription elongation factor 0003711 F transcription elongation factor 0008023 C transcription elongation factor complex 24 0006891 P intra-Golgi transport 0005083 F small GTPase regulatory/interacting protein 0005085 F guanyl-nucleotide exchange factor

Page 34: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

34

25 0005936 C shmoo 0005937 C shmoo tip 26 0016571 P histone methylation 0000183 P chromatin silencing at ribosomal DNA (rDNA) 27 0000209 P polyubiquitination 0006513 P monoubiquitination 28 0000272 P polysaccharide catabolism 0006457 P protein folding 29 0009250 P glucan biosynthesis 0006073 P glucan metabolism 30 0006643 P membrane lipid metabolism 0006644 P phospholipid metabolism 31 0016278 F lysine N-methyltransferase 0016279 F protein-lysine N-methyltransferase 32 0005777 C peroxisome 33 0015662 F P-type ATPase 34 0006267 P pre-replicative complex formation and maintenance 35 0003714 F transcription co-repressor 36 0000147 P actin cortical patch assembly 37 0000086 P G2/M transition of mitotic cell cycle 38 0004576 F oligosaccharyl transferase 39 0000131 C incipient bud site 40 0009277 C cell wall (sensu Fungi) 41 0006368 P RNA elongation from Pol II promoter 42 0003899 F DNA-directed RNA polymerase

Page 35: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

35

Table S8. A defined subset of GO functional annotations used to assign a general function to each gene in the genetic interaction dataset of Table S1.

Simplified GO Functional Role Aging Amino-acid metabolism Carbohydrate metabolism Cell cycle control Cell growth and/or maintenance Cell polarity Cell stress Cell structure Cell wall organization and biogenesis Chromatin/chromosome structure Cytokinesis Differentiation DNA repair DNA replication Endocytosis Energy generation ER organization and biogenesis Glycogen metabolism Lipid metabolism Mating response Meiosis Metabolism Mitochondrion organization and biogenesis Mitosis Nuclear-cytoplasmic transport Other metabolism Peroxisome organization and biogenesis Phosphate metabolism Pol I transcription Pol II transcription Protein degradation Protein folding Protein modification Protein synthesis Protein targeting Protein translocation Recombination Ribosomal large subunit assembly and maintenance Ribosomal large subunit nucleus export RNA metabolism RNA processing RNA splicing RNA turnover Signal transduction Small molecule transport Transport tRNA methylation Unknown Vacuolar organization and biogenesis Vesicular transport

Page 36: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

36

References S1. A. H. Tong et al., Science 294, 2364 (2001). S2. H. Ding et al., (in preparation). S3. C. B. Brachmann et al., Yeast 14, 115 (1998). S4. R. S. Sikorski, P. Hieter, Genetics 122, 19 (1989). S5. A. S. Goehring et al., Mol Biol Cell 14, 1501 (2003). S6. K. G. Kozminski et al., Mol Biol Cell 14, 4958 (2003). S7. N. J. Krogan et al., Mol Cell Biol 23, 4207 (2003). S8. M. Bellaoui et al., Embo J 22, 4304 (2003). S9. D. Huang, J. Moffat, B. Andrews, Mol Cell Biol 22, 5076 (2002). S10. P. Shannon et al., Genome Res 13, 2498 (2003). S11. T. I. Lee et al., Science 298, 799 (2002). S12. C. von Mering et al., Nature 417, 399 (2002). S13. H. W. Mewes et al., Nucleic Acids Res 30, 31 (2002). S14. R. J. Cho et al., Mol Cell 2, 65 (1998). S15. T. R. Hughes et al., Cell 102, 109 (2000). S16. D. S. Goldberg, F. P. Roth, Proc Natl Acad Sci U S A 100, 4372 (2003). S17. P. Uetz et al., Nature 403, 623 (2000). S18. T. Ito et al., Proc Natl Acad Sci U S A 98, 4569 (2001). S19. A. C. Gavin et al., Nature 415, 141 (2002). S20. Y. Ho et al., Nature 415, 180 (2002). S21. G. D. Bader, C. W. Hogue, Nat Biotechnol 20, 991 (2002). S22. K. D. Pruitt, D. R. Maglott, Nucleic Acids Res 29, 137 (2001). S23. S. F. Altschul et al., Nucleic Acids Res 25, 3389 (1997). S24. T. G. O. Consortium. (2003), vol. 2003. S25. G. D. Bader, C. W. Hogue, BMC Bioinformatics 4, 2 (2003). S26. M. Ashburner et al., Nat Genet 25, 25 (2000). S27. O. K. GF Berriz, B Bryant, C Sander, and FP Roth., Bioinformatics (in press). S28. K. A. Kosco et al., Mol Biol Cell 12, 2870 (2001). S29. W. L. Lee, J. R. Oberle, J. A. Cooper, J Cell Biol 160, 355 (2003). S30. A. L. Goldstein, J. H. McCusker, Yeast 15, 1541 (1999). S31. D. Pasqualone, T. C. Huffaker, J Cell Biol 127, 1973 (1994). S32. S. Itzkovitz, R. Milo, N. Kashtan, G. Ziv, U. Alon, Phys Rev E Stat Nonlin Soft

Matter Phys 68, 026127 (2003). S33. A. Grigoriev, Nucleic Acids Res 31, 4157 (2003). S34. J. L. Badano, N. Katsanis, Nat Rev Genet 3, 779 (2002).

Page 37: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

The "Query Gene" column indicates the gene used as query in a SGA screen.The "Genetic Interaction - Gene Name" column indicates the gene identified as an interactor with a particular query.The "Genetic Interaction - Systematic Name" column indicates the systematic (ORF) name that corresponds to the interactor gene.The "Score" column is defined as follows:An interaction scored three times in the three runs by visual inspection received a score of "3".An interaction scored twice in the three runs by visual inspection received a score of "2".An interaction scored by the computer-based image analysis but not visual inspection received a score of "1".For interactions that scored once in the three runs by visual inspection, confirmation was attempted only for those gene pairs with related functions. Such confirmed interactions received a score of "0".

The "RSA" column identifies an interaction that was confirmed by random spore analysis.The "Tetrad" column indentifies an interaction confirmed by tetrad analysis."SS" refers to a synthetic sick interaction."SL" refers to a synthetic lethal interaction.The "Functional Role" column indicates the assigned GO functional annotation from our defined subset of annotations.All the interactions are identified in this study unless otherwise stated.References: Genetic Interactions that have been previously described.A. H. Tong et al. , Science 294, 2364 (2001)A. S. Goehring et al. , Mol. Biol. Cell , 14,1501 (2003)K. Kozminski et al. , Mol. Biol. Cell , 14,4958 (2003)N. Krogan et al. , Mol. Cell Biol. , 23, 4207 (2003)M. Bellaoui et al. , EMBO , 22, 4304 (2003)D. Huang et al. , Mol. Cell Biol. , 22, 5076 (2003)

Query Gene

Genetic Interaction - Gene Name

Genetic Interaction - Systematic Name Score RSA Tetrad Functional Role Reference

BNI1 PCL1 YNL289W 3 SS Cell cycle control Tong, 2001BNI1 SWE1 YJL187C 0 SS Cell cycle control Tong, 2001BNI1 SWI4 YER111C 0 SL Cell cycle controlBNI1 BBC1 YJL020C 2 SS Cell polarity Tong, 2001BNI1 BEM1 YBR200W 3 SL Cell polarity Tong, 2001BNI1 BEM2 YER155C 3 SL Cell polarity Tong, 2001BNI1 BEM4 YPL161C 3 SS Cell polarity Tong, 2001BNI1 BUD6 YLR319C 3 SS Cell polarity Tong, 2001BNI1 CLA4 YNL298W 3 SL Cell polarity Tong, 2001BNI1 ELM1 YKL048C 3 SS Cell polarity Tong, 2001BNI1 GIN4 YDR507C 2 SL Cell polarity Tong, 2001BNI1 NAP1 YKR048C 3 SS Cell polarity Tong, 2001BNI1 NBP2 YDR162C 3 SS Cell polarity Tong, 2001BNI1 SLA1 YBL007C 3 SS Cell polarity Tong, 2001BNI1 ATS1 YAL020C 0 SL Cell structure Tong, 2001BNI1 SAC3 YDR159W 0 SS Cell structureBNI1 YKE2 YLR200W 3 SS Cell structure Tong, 2001BNI1 BCK1 YJL095W 3 SL Cell wall organization and biogenesis Tong, 2001BNI1 CHS3 YBR023C 3 SS Cell wall organization and biogenesis Tong, 2001BNI1 CHS5 YLR330W 3 SS Cell wall organization and biogenesis Tong, 2001BNI1 CHS7 YHR142W 3 SS Cell wall organization and biogenesis Tong, 2001BNI1 SKT5 YBL061C 3 SS Cell wall organization and biogenesis Tong, 2001BNI1 SLT2 YHR030C 3 SL Cell wall organization and biogenesis Tong, 2001BNI1 SMI1 YGR229C 3 SL Cell wall organization and biogenesis Tong, 2001BNI1 BNI4 YNL233W 3 SS Cytokinesis Tong, 2001BNI1 BNR1 YIL159W 3 SL Cytokinesis Tong, 2001BNI1 CYK3 YDL117W 3 SS Cytokinesis Tong, 2001BNI1 SHS1 YDL225W 2 SL Cytokinesis Tong, 2001BNI1 ERG2 YMR202W 0 SS Lipid metabolism

Page 38: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

BNI1 ERG3 YLR056W 0 SS Lipid metabolismBNI1 FAB1 YFR019W 3 SL Lipid metabolism Tong, 2001BNI1 MDM20 YOL076W 0 SS Mitochondrion organization and biogenesisBNI1 ARP1 YHR129C 3 SL Mitosis Tong, 2001BNI1 ASE1 YOR058C 2 SL Mitosis Tong, 2001BNI1 DYN1 YKR054C 3 SL Mitosis Tong, 2001BNI1 DYN2 YDR424C 3 SS Mitosis Tong, 2001BNI1 JNM1 YMR294W 3 SL Mitosis Tong, 2001BNI1 NIP100 YPL174C 3 SL Mitosis Tong, 2001BNI1 NUM1 YDR150W 3 SL Mitosis Tong, 2001BNI1 PAC1 YOR269W 3 SL Mitosis Tong, 2001BNI1 PAC11 YDR488C 2 SL Mitosis Tong, 2001BNI1 ELP2 YGR200C 3 SL Pol II transcription Tong, 2001BNI1 ELP3 YPL086C 3 SS Pol II transcription Tong, 2001BNI1 ELP4 YPL101W 0 SL Pol II transcriptionBNI1 ELP6 YMR312W 0 SL Pol II transcriptionBNI1 UBA4 YHR111W 3 SS Protein modification Tong, 2001BNI1 PIN4 YBL051C 3 SL RNA processing Tong, 2001BNI1 TIP41 YPR040W 0 SS Signal transductionBNI1 KRE24 YPL102C 0 SL UnknownBNI1 MMR1 YLR190W 3 SS Unknown Tong, 2001BNI1 TUS1 YLR425W 3 SS Unknown Tong, 2001BNI1 YBL062W YBL062W 3 SS Unknown Tong, 2001BNI1 YDR149C YDR149C 3 SL Unknown Tong, 2001BNI1 YGR228W YGR228W 0 SL UnknownBNI1 YKR047W YKR047W 3 SS Unknown Tong, 2001BNI1 YLL049W YLL049W 0 SS UnknownBNI1 YMR299C YMR299C 3 SL Mitosis Tong, 2001BNI1 YNL119W YNL119W 3 SS Unknown Tong, 2001BNI1 YOR322C YOR322C 0 SS UnknownBNI1 VID22 YLR373C 0 SL Vacuolar organization and biogenesisBNI1 VPS67 YKR020W 0 SS Vacuolar organization and biogenesisBNI1 DRS2 YAL026C 3 SL Vesicular transport Tong, 2001BNI1 SNC2 YOR327C 3 SL Vesicular transport Tong, 2001BNI1 VPS28 YPL065W 3 SL Vesicular transport Tong, 2001BNI1 YPT6 YLR262C 3 SS Vesicular transport Tong, 2001BBC1 CAP1 YKL007W 3 SS Cell structure Tong, 2001BBC1 CAP2 YIL034C 3 SS Cell structure Tong, 2001BBC1 PAC10 YGR078C 3 SS Cell structure Tong, 2001BBC1 GIM3 YNL153C 3 SL Cell structure Tong, 2001BBC1 GIM5 YML094W 3 SL Cell structure Tong, 2001BBC1 SAC6 YDR129C 3 SL Cell structure Tong, 2001BBC1 BEM1 YBR200W 3 SL Cell polarity Tong, 2001BBC1 BEM4 YPL161C 3 SL Cell polarity Tong, 2001BBC1 BNI1 YNL271C 3 SS Cell polarity Tong, 2001BBC1 SLA1 YBL007C 3 SS Cell polarity Tong, 2001BBC1 CHS5 YLR330W 3 SS Cell wall organization and biogenesis Tong, 2001BBC1 RAS2 YNL098C 3 SL Signal transduction Tong, 2001BBC1 ELP2 YGR200C 3 SL Pol II transcription Tong, 2001BBC1 ELP3 YPL086C 0 SS Pol II transcription Tong, 2001BBC1 SDS3 YIL084C 2 SL Chromatin/chromosome structure Tong, 2001BBC1 YLR235C YLR235C 3 SL Unknown Tong, 2001BBC1 YML095C-A YML095C-A 2 SL Unknown Tong, 2001NBP2 BIM1 YER016W 3 SL Mitosis Tong, 2001NBP2 CIN2 YPL241C 3 SS Cell structure Tong, 2001NBP2 KAR9 YPL269W 3 SL Mitosis Tong, 2001NBP2 KIP3 YGL216W 3 SL Mitosis Tong, 2001NBP2 PAC10 YGR078C 3 SS Cell structure Tong, 2001NBP2 GIM5 YML094W 3 SL Cell structure Tong, 2001NBP2 CAP1 YKL007W 3 SS Cell structure Tong, 2001NBP2 CAP2 YIL034C 2 SS Cell structure Tong, 2001

Page 39: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

NBP2 BNI1 YNL271C 3 SS Cell polarity Tong, 2001NBP2 FAB1 YFR019W 3 SL Lipid metabolism Tong, 2001NBP2 SMI1 YGR229C 3 SS Cell wall organization and biogenesis Tong, 2001NBP2 VAM7 YGL212W 3 SS Vacuolar organization and biogenesis Tong, 2001NBP2 VPS29 YHR012W 3 SS Vesicular transport Tong, 2001NBP2 RPL16A YIL133C 3 SS Protein synthesis Tong, 2001NBP2 RPS18B YML026C 3 SS Protein synthesis Tong, 2001NBP2 RPS23A YGR118W 3 SS Protein synthesis Tong, 2001NBP2 CPR6 YLR216C 3 SS Protein folding Tong, 2001NBP2 FPR1 YNL135C 3 SS Protein folding Tong, 2001NBP2 CLB4 YLR210W 3 SS Cell cycle control Tong, 2001NBP2 RTT109 YLL002W 3 SS DNA repair Tong, 2001NBP2 RTG2 YGL252C 2 SS Carbohydrate metabolism Tong, 2001NBP2 RTG3 YBL103C 3 SS Pol II transcription Tong, 2001NBP2 MON1 YGL124C 3 SS Unknown Tong, 2001NBP2 YDL063C YDL063C 3 SS Unknown Tong, 2001NBP2 YGL211W YGL211W 2 SS Unknown Tong, 2001NBP2 YGL217C YGL217C 3 SL Unknown Tong, 2001NBP2 YML095C-A YML095C-A 0 SL Unknown Tong, 2001BIM1 DEP1 YAL013W 1 SL Lipid metabolismBIM1 RXT2 YBR095C 0 SL Unknown Tong, 2001BIM1 IML3 YBR107C 2 SL Chromatin/chromosome structure Tong, 2001BIM1 BEM1 YBR200W 2 SL Cell polarity Tong, 2001BIM1 AOR1 YBR231C 0 SL Unknown Tong, 2001BIM1 DCC1 YCL016C 2 SL Chromatin/chromosome structure Tong, 2001BIM1 BIK1 YCL029C 2 SL Mitosis Tong, 2001BIM1 MRC1 YCL060C 2 SL DNA repair Tong, 2001BIM1 CYK3 YDL117W 3 SS CytokinesisBIM1 SHS1 YDL225W 1 SS CytokinesisBIM1 RAD61 YDR014W 1 SL UnknownBIM1 YDR149C YDR149C 1 SL Unknown Tong, 2001BIM1 NUM1 YDR150W 0 SL Mitosis Tong, 2001BIM1 SAC3 YDR159W 0 SL Cell structureBIM1 NBP2 YDR162C 2 SS Cell polarity Tong, 2001BIM1 CHL4 YDR254W 2 SL Chromatin/chromosome structure Tong, 2001BIM1 RTT103 YDR289C 0 SS Unknown Tong, 2001BIM1 IPK1 YDR315C 0 SL Lipid metabolismBIM1 MCM21 YDR318W 1 SL Chromatin/chromosome structure Tong, 2001BIM1 MSN5 YDR335W 0 SS Nuclear-cytoplasmic transportBIM1 VID21 YDR359C 0 SL UnknownBIM1 YDR360W YDR360W 1 SL UnknownBIM1 NKP1 YDR383C 0 SS Chromatin/chromosome structureBIM1 DYN2 YDR424C 1 SL MitosisBIM1 PAC11 YDR488C 0 SL Mitosis Tong, 2001BIM1 GIM4 YEL003W 1 SL Cell structure Tong, 2001BIM1 CIN8 YEL061C 0 SS MitosisBIM1 FAB1 YFR019W 0 SL Lipid metabolism Tong, 2001BIM1 MAD1 YGL086W 3 SL Mitosis Tong, 2001BIM1 RAD54 YGL163C 1 SL DNA repair Tong, 2001BIM1 KEM1 YGL173C 1 SL RNA processing Tong, 2001BIM1 YGL211W YGL211W 1 SS Unknown Tong, 2001BIM1 KIP3 YGL216W 1 SL Mitosis Tong, 2001BIM1 YGL217C YGL217C 0 SL Unknown Tong, 2001BIM1 PAC10 YGR078C 0 SL Cell structureBIM1 BUB1 YGR188C 0 SL Mitosis Tong, 2001BIM1 ELP2 YGR200C 3 SL Pol II transcription Tong, 2001BIM1 YGR228W YGR228W 0 SL UnknownBIM1 SMI1 YGR229C 3 SL Cell wall organization and biogenesis Tong, 2001BIM1 YTA7 YGR270W 0 SL Vacuolar organization and biogenesis Tong, 2001BIM1 UBA4 YHR111W 0 SS UnknownBIM1 ARP1 YHR129C 0 SL Mitosis Tong, 2001

Page 40: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

BIM1 CTF8 YHR191C 0 SL Chromatin/chromosome structure Tong, 2001BIM1 MAD3 YJL013C 3 SL Mitosis Tong, 2001BIM1 MAD2 YJL030W 3 SL Mitosis Tong, 2001BIM1 LSM1 YJL124C 1 SL RNA turnoverBIM1 BFA1 YJR053W 2 SL Mitosis Tong, 2001BIM1 MCM22 YJR135C 3 SL Chromatin/chromosome structure Tong, 2001BIM1 ELM1 YKL048C 0 SL Cell polarityBIM1 KTI12 YKL110C 1 SS UnknownBIM1 DYN1 YKR054C 2 SL Mitosis Tong, 2001BIM1 YLL049W YLL049W 1 SL UnknownBIM1 ARP6 YLR085C 0 SS Cell structure Tong, 2001BIM1 MMR1 YLR190W 0 SS UnknownBIM1 YKE2 YLR200W 0 SL Cell structureBIM1 YPT6 YLR262C 0 SS Vesicular transportBIM1 NKP2 YLR315W 0 SS Chromatin/chromosome structureBIM1 VID22 YLR373C 0 SL Vacuolar organization and biogenesis Tong, 2001BIM1 CTF3 YLR381W 3 SL Chromatin/chromosome structure Tong, 2001BIM1 IKI3 YLR384C 1 SS Pol II transcriptionBIM1 VAC14 YLR386W 0 SL Vacuolar organization and biogenesis Tong, 2001BIM1 PPZ1 YML016C 0 SL Signal transduction Tong, 2001BIM1 RAD52 YML032C 0 SS DNA repairBIM1 YML094C-A YML094C-A 0 SL Unknown Tong, 2001BIM1 GIM5 YML094W 1 SL Cell structure Tong, 2001BIM1 TUB3 YML124C 0 SL Cell structureBIM1 CSM3 YMR048W 1 SL Meiosis Tong, 2001BIM1 BUB2 YMR055C 3 SL Mitosis Tong, 2001BIM1 CTF18 YMR078C 0 SL Chromatin/chromosome structureBIM1 MRE11 YMR224C 0 SL DNA repairBIM1 SAP30 YMR263W 0 SL Chromatin/chromosome structure Tong, 2001BIM1 JNM1 YMR294W 2 SL Mitosis Tong, 2001BIM1 YMR299C YMR299C 1 SL MitosisBIM1 ELP6 YMR312W 1 SL Pol II transcriptionBIM1 PHO23 YNL097C 0 SL Phosphate metabolism Tong, 2001BIM1 INP52 YNL106C 1 SL Lipid metabolism Tong, 2001BIM1 YNL136W YNL136W 1 SS UnknownBIM1 GIM3 YNL153C 2 SL Cell structure Tong, 2001BIM1 YNL170W YNL170W 2 SL Unknown Tong, 2001BIM1 YNL201C YNL201C 1 SS Carbohydrate metabolismBIM1 IES2 YNL215W 0 SS Unknown Tong, 2001BIM1 TOF1 YNL273W 3 SL DNA repairBIM1 CLA4 YNL298W 2 SL Cell polarityBIM1 MCK1 YNL307C 0 SL Meiosis Tong, 2001BIM1 BRE5 YNR051C 0 SL UnknownBIM1 HTZ1 YOL012C 0 SL Chromatin/chromosome structureBIM1 BUB3 YOR026W 0 SL Mitosis Tong, 2001BIM1 ASE1 YOR058C 1 SL Mitosis Tong, 2001BIM1 SLK19 YOR195W 3 SL Chromatin/chromosome structure Tong, 2001BIM1 PAC1 YOR269W 2 SL Mitosis Tong, 2001BIM1 CIN1 YOR349W 0 SL Cell structureBIM1 CHL1 YPL008W 2 SL Chromatin/chromosome structureBIM1 YPL017C YPL017C 3 SL Unknown Tong, 2001BIM1 CTF19 YPL018W 3 SL Chromatin/chromosome structure Tong, 2001BIM1 ELP3 YPL086C 2 SS Pol II transcriptionBIM1 ELP4 YPL101W 2 SL Pol II transcriptionBIM1 KRE24 YPL102C 2 SL UnknownBIM1 KIP2 YPL155C 2 SL MitosisBIM1 NIP100 YPL174C 1 SL MitosisBIM1 MCM16 YPR046W 3 SL Chromatin/chromosome structureBIM1 CTF4 YPR135W 0 SL Chromatin/chromosome structureBIM1 MMS1 YPR164W 0 SL DNA repairARC40 BCK1 YJL095W 2 SL Cell wall organization and biogenesis Tong, 2001

Page 41: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

ARC40 BNI4 YNL233W 3 SS Cytokinesis Tong, 2001ARC40 CHS3 YBR023C 3 SL Cell wall organization and biogenesis Tong, 2001ARC40 SKT5 YBL061C 3 SS Cell wall organization and biogenesis Tong, 2001ARC40 CHS5 YLR330W 3 SS Cell wall organization and biogenesis Tong, 2001ARC40 CHS6 YJL099W 0 SL Cell wall organization and biogenesis Tong, 2001ARC40 CHS7 YHR142W 3 SS Cell wall organization and biogenesis Tong, 2001ARC40 HOC1 YJR075W 2 SL Cell wall organization and biogenesis Tong, 2001ARC40 KRE1 YNL322C 3 SL Cell wall organization and biogenesis Tong, 2001ARC40 SLT2 YHR030C 3 SL Cell wall organization and biogenesis Tong, 2001ARC40 SPF1 YEL031W 3 SS Small molecule transport Tong, 2001ARC40 RMD7 YER083C 0 SS Cell wall organization and biogenesis Tong, 2001ARC40 ARC18 YLR370C 0 SL Cell polarity Tong, 2001ARC40 BEM1 YBR200W 3 SL Cell polarity Tong, 2001ARC40 BEM2 YER155C 3 SL Cell polarity Tong, 2001ARC40 CLA4 YNL298W 3 SL Cell polarity Tong, 2001ARC40 MYO5 YMR109W 2 SS Cell polarity Tong, 2001ARC40 PEA2 YER149C 0 SS Cell polarity Tong, 2001ARC40 VRP1 YLR337C 3 SL Cell polarity Tong, 2001ARC40 YKE2 YLR200W 3 SS Cell structure Tong, 2001ARC40 GIM3 YNL153C 3 SL Cell structure Tong, 2001ARC40 GIM4 YEL003W 3 SL Cell structure Tong, 2001ARC40 SAC6 YDR129C 3 SL Cell structure Tong, 2001ARC40 GLO3 YER122C 3 SL Vesicular transport Tong, 2001ARC40 SAP155 YFR040W 3 SS Cell cycle control Tong, 2001ARC40 SEC66 YBR171W 2 SL Vesicular transport Tong, 2001ARC40 ILM1 YJR118C 2 SL Energy generation Tong, 2001ARC40 MNN11 YJL183W 3 SL Protein modification Tong, 2001ARC40 STE24 YJR117W 3 SS Protein modification Tong, 2001ARC40 CIK1 YMR198W 0 SS Mitosis Tong, 2001ARC40 RIM101 YHL027W 3 SS Meiosis Tong, 2001ARC40 RUD3 YOR216C 3 SL Vesicular transport Tong, 2001ARC40 SEC22 YLR268W 3 SL Vesicular transport Tong, 2001ARC40 TFP3 YPL234C 2 SL Vacuolar organization and biogenesis Tong, 2001ARC40 CPR7 YJR032W 3 SS Protein folding Tong, 2001ARC40 SHE4 YOR035C 3 SL Differentiation Tong, 2001ARC40 SUM1 YDR310C 2 SS Chromatin/chromosome structure Tong, 2001ARC40 YBL062W YBL062W 0 SS Unknown Tong, 2001ARC40 YLR111W YLR111W 2 SS Unknown Tong, 2001ARP2 BCK1 YJL095W 3 SL Cell wall organization and biogenesis Tong, 2001ARP2 BNI4 YNL233W 3 SS Cytokinesis Tong, 2001ARP2 CHS3 YBR023C 3 SL Cell wall organization and biogenesis Tong, 2001ARP2 SKT5 YBL061C 3 SS Cell wall organization and biogenesis Tong, 2001ARP2 CHS5 YLR330W 0 SS Cell wall organization and biogenesis Tong, 2001ARP2 CHS6 YJL099W 3 SL Cell wall organization and biogenesis Tong, 2001ARP2 CHS7 YHR142W 3 SS Cell wall organization and biogenesis Tong, 2001ARP2 HOC1 YJR075W 0 SL Cell wall organization and biogenesis Tong, 2001ARP2 KRE1 YNL322C 3 SL Cell wall organization and biogenesis Tong, 2001ARP2 SLT2 YHR030C 3 SL Cell wall organization and biogenesis Tong, 2001ARP2 SPF1 YEL031W 3 SS Small molecule transport Tong, 2001ARP2 RMD7 YER083C 3 SL Cell wall organization and biogenesis Tong, 2001ARP2 BEM1 YBR200W 2 SL Cell polarity Tong, 2001ARP2 BEM2 YER155C 3 SL Cell polarity Tong, 2001ARP2 CLA4 YNL298W 3 SL Cell polarity Tong, 2001ARP2 PEA2 YER149C 3 SS Cell polarity Tong, 2001ARP2 PRK1 YIL095W 2 SS Cell polarity Tong, 2001ARP2 RGD1 YBR260C 2 SS Cell polarity Tong, 2001ARP2 RVS161 YCR009C 3 SL Cell polarity Tong, 2001ARP2 RVS167 YDR388W 2 SS Cell polarity Tong, 2001ARP2 VRP1 YLR337C 2 SL Cell polarity Tong, 2001ARP2 YKE2 YLR200W 2 SS Cell structure Tong, 2001ARP2 PAC10 YGR078C 0 SS Cell structure Tong, 2001

Page 42: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

ARP2 GIM3 YNL153C 3 SL Cell structure Tong, 2001ARP2 GIM4 YEL003W 3 SL Cell structure Tong, 2001ARP2 SAC6 YDR129C 0 SL Cell structure Tong, 2001ARP2 SAC7 YDR389W 0 SS Cell structure Tong, 2001ARP2 ILM1 YJR118C 3 SL Energy generation Tong, 2001ARP2 SAP155 YFR040W 0 SS Cell cycle control Tong, 2001ARP2 SEC66 YBR171W 3 SL Vesicular transport Tong, 2001ARP2 MNN11 YJL183W 3 SL Protein modification Tong, 2001ARP2 STE24 YJR117W 3 SS Protein modification Tong, 2001ARP2 BTS1 YPL069C 3 SL Protein modification Tong, 2001ARP2 RUD3 YOR216C 0 SL Vesicular transport Tong, 2001ARP2 CPR7 YJR032W 3 SS Protein folding Tong, 2001ARP2 SHE4 YOR035C 3 SL Differentiation Tong, 2001ARP2 SUM1 YDR310C 3 SS Chromatin/chromosome structure Tong, 2001ARP2 SRO9 YCL037C 0 SL Protein synthesis Tong, 2001ARP2 UTH1 YKR042W 0 SS Aging Tong, 2001ARP2 DEP1 YAL013W 2 SL Lipid metabolism Tong, 2001ARP2 YBL062W YBL062W 3 SS Unknown Tong, 2001ARP2 YDR018C YDR018C 0 SL Unknown Tong, 2001ARP2 YGL250W YGL250W 3 SS Unknown Tong, 2001ARP2 YLR111W YLR111W 3 SS Unknown Tong, 2001SGS1 MMS4 YBR098W 3 SL DNA repair Tong, 2001SGS1 MUS81 YDR386W 3 SL DNA repair Tong, 2001SGS1 SAE2 YGL175C 3 SL DNA repair Tong, 2001SGS1 RAD50 YNL250W 3 SL DNA repair Tong, 2001SGS1 HPR5 YJL092W 3 SL DNA repair Tong, 2001SGS1 ASF1 YJL115W 3 SS Chromatin/chromosome structure Tong, 2001SGS1 RAD27 YKL113C 2 SL DNA repair Tong, 2001SGS1 SLX1 YBR228W 3 SL DNA repair Tong, 2001SGS1 SLX4 YLR135W 2 SL DNA repair Tong, 2001SGS1 WSS1 YHR134W 3 SL DNA repair Tong, 2001SGS1 POL32 YJR043C 3 SL DNA replication Tong, 2001SGS1 RNR1 YER070W 0 SL DNA replication Tong, 2001SGS1 RRM3 YHR031C 3 SL DNA replication Tong, 2001SGS1 MGS1 YNL218W 3 SS DNA replication Tong, 2001SGS1 CSM3 YMR048W 2 SL Meiosis Tong, 2001SGS1 ESC2 YDR363W 0 SS Chromatin/chromosome structure Tong, 2001SGS1 RTT107 YHR154W 3 SS Chromatin/chromosome structure Tong, 2001SGS1 TOP1 YOL006C 0 SS Chromatin/chromosome structure Tong, 2001SGS1 SWE1 YJL187C 0 SS Cell cycle control Tong, 2001SGS1 PUB1 YNL016W 2 SS RNA processing Tong, 2001SGS1 RPL24A YGL031C 3 SS Protein synthesis Tong, 2001SGS1 SIS2 YKR072C 2 SS Cell stress Tong, 2001SGS1 SOD1 YJR104C 3 SL Cell stress Tong, 2001SGS1 YBR094W YBR094W 3 SL Unknown Tong, 2001SGS1 CTF18 YMR078C 0 SL Chromatin/chromosome structureRAD27 MMS4 YBR098W 0 SS DNA repair Tong, 2001RAD27 MUS81 YDR386W 3 SL DNA repair Tong, 2001RAD27 SAE2 YGL175C 3 SL DNA repair Tong, 2001RAD27 RAD50 YNL250W 0 SL DNA repair Tong, 2001RAD27 HPR5 YJL092W 3 SL DNA repair Tong, 2001RAD27 DDC1 YPL194W 3 SS DNA repair Tong, 2001RAD27 CAC2 YML102W 3 SS Chromatin/chromosome structure Tong, 2001RAD27 EXO1 YOR033C 3 SS DNA repair Tong, 2001RAD27 MRE11 YMR224C 0 SL DNA repair Tong, 2001RAD27 RAD9 YDR217C 3 SL DNA repair Tong, 2001RAD27 RAD17 YOR368W 3 SS DNA repair Tong, 2001RAD27 RAD24 YER173W 3 SS DNA repair Tong, 2001RAD27 RAD51 YER095W 3 SL DNA repair Tong, 2001RAD27 RAD52 YML032C 3 SL DNA repair Tong, 2001RAD27 RAD54 YGL163C 0 SL DNA repair Tong, 2001

Page 43: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

RAD27 RAD55 YDR076W 3 SL DNA repair Tong, 2001RAD27 RAD57 YDR004W 3 SL DNA repair Tong, 2001RAD27 SGS1 YMR190C 0 SL DNA repair Tong, 2001RAD27 XRS2 YDR369C 3 SL DNA repair Tong, 2001RAD27 CTF4 YPR135W 0 SS Chromatin/chromosome structure Tong, 2001RAD27 RPL27A YHR010W 3 SL Protein synthesis Tong, 2001RAD27 RPS30B YOR182C 0 SS Protein synthesis Tong, 2001RAD27 DOC1 YGL240W 0 SL Cell cycle control Tong, 2001RAD27 ESC2 YDR363W 0 SS Chromatin/chromosome structure Tong, 2001RAD27 HST1 YOL068C 0 SS Chromatin/chromosome structure Tong, 2001RAD27 HPC2 YBR215W 0 SS Pol II transcription Tong, 2001RAD27 CSM3 YMR048W 3 SL Meiosis Tong, 2001RAD27 LYS7 YMR038C 0 SL Amino-acid metabolism Tong, 2001RAD27 SIS2 YKR072C 3 SS Cell stress Tong, 2001RAD27 SOD1 YJR104C 3 SL Cell stress Tong, 2001RAD27 YDJ1 YNL064C 0 SL Mitochondrion organization and biogenesis Tong, 2001RAD27 HST3 YOR025W 3 SS Chromatin/chromosome structure Tong, 2001RAD27 FYV11 YFL023W 3 SL Unknown Tong, 2001RAD27 YLR352W YLR352W 0 SS Unknown Tong, 2001RAD27 YNL171C YNL171C 0 SL Unknown Tong, 2001RAD27 YPR116W YPR116W 0 SL Unknown Tong, 2001RAD27 CTF18 YMR078C 0 SS Chromatin/chromosome structureCLA4 EDE1 YBL047C 3 SL Vesicular transport Goehring, 2003CLA4 SKT5 YBL061C 3 SL Cell wall organization and biogenesis Goehring, 2003CLA4 YBL062W YBL062W 3 SL Unknown Goehring, 2003CLA4 RPL23A YBL087C 3 SS Protein synthesis Goehring, 2003CLA4 CHS3 YBR023C 3 SL Cell wall organization and biogenesis Goehring, 2003CLA4 RPL19A YBR084C-A 3 SL Protein synthesis Goehring, 2003CLA4 RXT2 YBR095C 3 SL Unknown Goehring, 2003CLA4 YBR174C YBR174C 2 SL Unknown Goehring, 2003CLA4 SWD3 YBR175W 3 SL Chromatin/chromosome structure Goehring, 2003CLA4 BEM1 YBR200W 2 SL Cell polarity Goehring, 2003CLA4 DCC1 YCL016C 3 SL Chromatin/chromosome structure Goehring, 2003CLA4 RPL35A YDL191W 3 SL Protein synthesis Goehring, 2003CLA4 SHS1 YDL225W 0 SL Cytokinesis Goehring, 2003CLA4 SEM1 YDR363W-A 3 SL Vesicular transport Goehring, 2003CLA4 DYN2 YDR424C 2 SS Mitosis Goehring, 2003CLA4 SWI4 YER111C 3 SL Cell cycle control Goehring, 2003CLA4 PEA2 YER149C 3 SS Cell polarity Goehring, 2003CLA4 BEM2 YER155C 3 SL Cell polarity Goehring, 2003CLA4 FAB1 YFR019W 3 SL Lipid metabolism Goehring, 2003CLA4 RPL24A YGL031C 2 SL Protein synthesis Goehring, 2003CLA4 SSF73 YGL066W 3 SL Pol II transcription Goehring, 2003CLA4 ITC1 YGL133W 3 SL Chromatin/chromosome structure Goehring, 2003CLA4 RAD54 YGL163C 3 SS DNA repair Goehring, 2003CLA4 PRE9 YGR135W 3 SL Protein degradation Goehring, 2003CLA4 ELP2 YGR200C 3 SS Pol II transcription Goehring, 2003CLA4 SMI1 YGR229C 3 SL Cell wall organization and biogenesis Goehring, 2003CLA4 STE20 YHL007C 3 SL Mating response Goehring, 2003CLA4 SLT2 YHR030C 3 SL Cell wall organization and biogenesis Goehring, 2003CLA4 UBA4 YHR111W 0 SS Unknown Goehring, 2003CLA4 CHS7 YHR142W 3 SL Cell wall organization and biogenesis Goehring, 2003CLA4 SPO12 YHR152W 3 SL Meiosis Goehring, 2003CLA4 CTF8 YHR191C 3 SL Chromatin/chromosome structure Goehring, 2003CLA4 RPN10 YHR200W 3 SL Pol II transcription Goehring, 2003CLA4 HOS4 YIL112W 3 SL Chromatin/chromosome structure Goehring, 2003CLA4 MGA2 YIR033W 3 SL Chromatin/chromosome structure Goehring, 2003CLA4 RTT101 YJL047C 2 SS Protein modification Goehring, 2003CLA4 BCK1 YJL095W 3 SL Cell wall organization and biogenesis Goehring, 2003CLA4 CHS6 YJL099W 3 SL Cell wall organization and biogenesis Goehring, 2003CLA4 ASF1 YJL115W 3 SL Chromatin/chromosome structure Goehring, 2003

Page 44: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

CLA4 RPS21B YJL136C 3 SL Protein synthesis Goehring, 2003CLA4 IXR1 YKL032C 3 SS DNA repair Goehring, 2003CLA4 SPA2 YLL021W 3 SL Cell polarity Goehring, 2003CLA4 APC9 YLR102C 3 SL Cell cycle control Goehring, 2003CLA4 BUD6 YLR319C 3 SL Cell polarity Goehring, 2003CLA4 CHS5 YLR330W 3 SL Cell wall organization and biogenesis Goehring, 2003CLA4 VAC14 YLR386W 3 SL Vacuolar organization and biogenesis Goehring, 2003CLA4 GIM5 YML094W 3 SL Cell structure Goehring, 2003CLA4 YML095C-A YML095C-A 3 SL Unknown Goehring, 2003CLA4 CTF18 YMR078C 0 SL Chromatin/chromosome structure Goehring, 2003CLA4 UBP8 YMR223W 3 SL Protein modification Goehring, 2003CLA4 SAP30 YMR263W 3 SL Chromatin/chromosome structure Goehring, 2003CLA4 ELP6 YMR312W 2 SS Pol II transcription Goehring, 2003CLA4 FKH2 YNL068C 2 SS Pol II transcription Goehring, 2003CLA4 GIM3 YNL153C 2 SL Cell structure Goehring, 2003CLA4 RTT106 YNL206C 2 SS Unknown Goehring, 2003CLA4 URE2 YNL229C 3 SL Amino-acid metabolism Goehring, 2003CLA4 BNI1 YNL271C 3 SL Cell polarity Goehring, 2003CLA4 SLK19 YOR195W 3 SL Chromatin/chromosome structure Goehring, 2003CLA4 RIM20 YOR275C 3 SL Cell stress Goehring, 2003CLA4 YPL047W YPL047W 3 SL Unknown Goehring, 2003CLA4 BEM4 YPL161C 3 SL Cell polarity Goehring, 2003CLA4 NIP100 YPL174C 3 SL Mitosis Goehring, 2003CLA4 CTF4 YPR135W 3 SL Chromatin/chromosome structure Goehring, 2003SHS1 CYK3 YDL117W 3 SL CytokinesisSHS1 SWI4 YER111C 3 SL Cell cycle controlSHS1 BEM2 YER155C 3 SL Cell polaritySHS1 BNI4 YNL233W 3 SS CytokinesisSHS1 BNI1 YNL271C 3 SL Cell polaritySHS1 CLA4 YNL298W 3 SL Cell polaritySMY1 DRS2 YAL026C 0 SS Vesicular transportSMY1 SLA1 YBL007C 2 SS Cell polaritySMY1 SKT5 YBL061C 3 SS Cell wall organization and biogenesisSMY1 CHS3 YBR023C 3 SS Cell wall organization and biogenesisSMY1 BEM1 YBR200W 1 SL Cell polaritySMY1 SHS1 YDL225W 1 SS CytokinesisSMY1 SWI4 YER111C 1 SS Cell cycle controlSMY1 BEM2 YER155C 3 SL Cell polaritySMY1 BUB1 YGR188C 3 SL MitosisSMY1 CHS7 YHR142W 0 SS Cell wall organization and biogenesisSMY1 BNI4 YNL233W 0 SS CytokinesisSMY1 CLA4 YNL298W 2 SL Cell polaritySLT2 EDE1 YBL047c 3 SL Vesicular transportSLT2 CHS3 YBR023C 3 SL Cell wall organization and biogenesisSLT2 ECM33 YBR078W 3 SL Cell wall organization and biogenesisSLT2 SEC66 YBR171W 3 SL Vesicular transportSLT2 ROT2 YBR229C 3 SS Cell wall organization and biogenesisSLT2 SWI5 YDR146C 3 SS Pol II transcriptionSLT2 MNN10 YDR245W 3 SL Protein modificationSLT2 YPS7 YDR349C 3 SL Protein degradationSLT2 ERD1 YDR414c 3 SL Protein modificationSLT2 SWI4 YER111C 3 SL Cell cycle controlSLT2 BEM2 YER155C 3 SL Cell polaritySLT2 CWH41 YGL027C 3 SL Cell wall organization and biogenesisSLT2 RIM8 YGL045W 3 SL UnknownSLT2 HUR1 YGL168W 3 SS UnknownSLT2 KRE11 YGR166W 3 SL Cell wall organization and biogenesisSLT2 SMI1 YGR229C 3 SL Cell wall organization and biogenesisSLT2 GCN5 YGR252W 3 SS Pol II transcriptionSLT2 GGA2 YHR108w 3 SS Vesicular transportSLT2 YUR1 YJL139C 3 SL Cell wall organization and biogenesis

Page 45: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

SLT2 HOC1 YJR075W 3 SL Cell wall organization and biogenesisSLT2 YKL037W YKL037W 3 SL UnknownSLT2 FPS1 YLL043W 3 SL TransportSLT2 CHS5 YLR330W 3 SL Cell wall organization and biogenesisSLT2 FKS1 YLR342W 3 SL Cell wall organization and biogenesisSLT2 RIM13 YMR154C 3 SS MeiosisSLT2 TPM1 YNL079C 3 SL Cell structureSLT2 BNI4 YNL233W 3 SL CytokinesisSLT2 BNI1 YNL271C 3 SS Cell polaritySLT2 CLA4 YNL298W 3 SS Cell polaritySLT2 IRA2 YOL081W 3 SL Signal transductionSLT2 RIM20 YOR275C 3 SL Cell stressSLT2 YPL158C YPL158C 3 SS UnknownBNI4 EDE1 YBL047C 1 SS Vesicular transportBNI4 RGD1 YBR260C 1 SS SS Cell polarityBNI4 RVS161 YCR009C 0 SS Cell polarityBNI4 CYK3 YDL117W 0 SL CytokinesisBNI4 SHS1 YDL225W 0 SS CytokinesisBNI4 NBP2 YDR162C 2 SS Cell polarityBNI4 RVS167 YDR388W 0 SL Cell polarityBNI4 SMI1 YGR229C 3 SL Cell wall organization and biogenesisBNI4 SLT2 YHR030C 2 SL Cell wall organization and biogenesisBNI4 BCK1 YJL095W 2 SL Cell wall organization and biogenesisBNI4 ILM1 YJR118C 3 SL Energy generationBNI4 IXR1 YKL032C 2 SS DNA repairBNI4 SPA2 YLL021W 2 SS Cell polarityBNI4 VRP1 YLR337C 2 SL Cell polarityBNI4 FKS1 YLR342W 2 SL Cell wall organization and biogenesisBNI4 VAN1 YML115C 1 SL Protein modificationBNI4 BNI1 YNL271C 2 SS Cell polarityBNI4 BRE5 YNR051C 2 SS UnknownBNI4 YPL066W YPL066W 0 SS UnknownPHO85 SPT7 YBR081C 3 SL Chromatin/chromosome stucture Huang, 2003PHO85 BEM1 YBR200W 3 SL Cell polarity Huang, 2003PHO85 RGD1 YBR260C 3 SL Cell polarity Huang, 2003PHO85 SRB8 YCR081W 3 SL Pol II transcription Huang, 2003PHO85 BRE1 YDL074C 3 SL Chromatin/chromosome stucture Huang, 2003PHO85 NUM1 YDR150W 3 SL Mitosis Huang, 2003PHO85 UME6 YDR207C 3 SL Meiosis Huang, 2003PHO85 MNN10 YDR245W 3 SL Protein modification Huang, 2003PHO85 ERD1 YDR414C 3 SL Protein modification Huang, 2003PHO85 SSN2 YDR443C 3 SL Pol II transcription Huang, 2003PHO85 NHX1 YDR456W 3 SL Transport Huang, 2003PHO85 ANP1 YEL036C 3 SL Protein modification Huang, 2003PHO85 YER049W YER049W 3 SL Chromatin/chromosome stucture Huang, 2003PHO85 SHC1 YER096W 3 SL Meiosis Huang, 2003PHO85 SWI4 YER111C 3 SL Cell cycle control Huang, 2003PHO85 BEM2 YER155C 3 SL Cell polarity Huang, 2003PHO85 YGL015C YGL015C 3 SL Unknown Huang, 2003PHO85 PMR1 YGL167C 3 SL Small molecule transport Huang, 2003PHO85 PAC10 YGR078C 3 SL Cell structure Huang, 2003PHO85 SRB5 YGR104C 3 SL Pol II transcription Huang, 2003PHO85 CHO2 YGR157W 3 SL Lipid metabolism Huang, 2003PHO85 YGR161C YGR161C 3 SL Unknown Huang, 2003PHO85 WSC4 YHL028W 3 SL Cell wall organization and biogenesis Huang, 2003PHO85 VPS29 YHR012W 3 SL Vesicular transport Huang, 2003PHO85 SLT2 YHR030C 3 SL Cell wall organization and biogenesis Huang, 2003PHO85 PAN5 YHR063C 3 SL Unknown Huang, 2003PHO85 BCK1 YJL095W 3 SL Cell wall organization and biogenesis Huang, 2003PHO85 GSH1 YJL101C 3 SL Other metabolism Huang, 2003PHO85 VPS35 YJL154C 3 SL Vesicular transport Huang, 2003

Page 46: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

PHO85 OPI3 YJR073C 3 SL Lipid metabolism Huang, 2003PHO85 HOC1 YJR075W 3 SL Cell wall organization and biogenesis Huang, 2003PHO85 YJR142W YJR142W 3 SL Unknown Huang, 2003PHO85 YKE2 YLR200W 3 SL Cell structure Huang, 2003PHO85 FKS1 YLR342W 3 SL Cell wall organization and biogenesis Huang, 2003PHO85 VPS38 YLR360W 3 SL Vesicular transport Huang, 2003PHO85 ROM2 YLR371W 3 SL Cell wall organization and biogenesis Huang, 2003PHO85 SUR4 YLR372W 3 SL Lipid metabolism Huang, 2003PHO85 TUS1 YLR425W 3 SL Unknown Huang, 2003PHO85 VAN1 YML115C 3 SL Protein modification Huang, 2003PHO85 YML122C YML122C 3 SL Unknown Huang, 2003PHO85 EFR3 YMR212C 3 SL Other metabolism Huang, 2003PHO85 FKS3 YMR306W 3 SL Cell wall organization and biogenesis Huang, 2003PHO85 TPM1 YNL079C 3 SL Cell structure Huang, 2003PHO85 GCR2 YNL199C 3 SL Pol II Transcription Huang, 2003PHO85 BNI1 YNL271C 3 SL Cell polarity Huang, 2003PHO85 CLA4 YNL298W 3 SL Cell polarity Huang, 2003PHO85 LEM3 YNL323W 3 SL Signal transduction Huang, 2003PHO85 TAT2 YOL020W 3 SL Transport Huang, 2003PHO85 MCH4 YOL119C 3 SL Transport Huang, 2003PHO85 SMF1 YOL122C 3 SL Small molecule transport Huang, 2003PHO85 SLG1 YOR008C 3 SL Cell wall organization and biogenesis Huang, 2003PHO85 RTS1 YOR014W 3 SL Cell stress Huang, 2003PHO85 VAM3 YOR106W 3 SL Vesicular transport Huang, 2003PHO85 SFL1 YOR140W 3 SL Pol II transcription Huang, 2003PHO85 GCR1 YPL075W 3 SL Glycogen metabolism Huang, 2003PHO85 BEM4 YPL161C 3 SL Cell polarity Huang, 2003PHO85 VIK1 YPL253C 3 SL Mitosis Huang, 2003PHO85 HFI1 YPL254W 3 SL Pol II transcription Huang, 2003ARL3 VAM6 YDL077C 1 SS Vesicular transportARL3 ARF1 YDL192W 1 SS TransportARL3 GSS1 YDR108W 3 SL Vesicular transportARL3 VPS61 YDR136C 3 SL Vesicular transportARL3 RGP1 YDR137W 3 SL Vesicular transportARL3 SUM1 YDR310C 0 SS Chromatin/chromosome structureARL3 SWA2 YDR320C 1 SS Vesicular transportARL3 GDA1 YEL042W 0 SL Protein modificationARL3 GLO3 YER122C 3 SL Vesicular transportARL3 COG7 YGL005C 3 SL Vesicular transportARL3 SWF3 YGL020C 2 SL UnknownARL3 GOS1 YHL031C 3 SS Vesicular transportARL3 CPR7 YJR032W 2 SL Protein foldingARL3 YKL118W YKL118W 1 SS UnknownARL3 VPS67 YKR020W 3 SL Vacuolar organization and biogenesisARL3 RIC1 YLR039C 2 SL Vesicular transportARL3 VPS63 YLR261C 3 SL Vacuolar organization and biogenesisARL3 YPT6 YLR262C 3 SL Vesicular transportARL3 COG8 YML071C 3 SS Vesicular transportARL3 COG6 YNL041C 3 SL Vesicular transportARL3 COG5 YNL051W 3 SL Vesicular transportARL3 MON2 YNL297C 0 SS Vacuolar organization and biogenesisARL3 TLG2 YOL018C 0 SS Vesicular transportARL3 VAM10 YOR068C 3 SS Vacuolar organization and biogenesisARL3 VPS5 YOR069W 3 SS Vesicular transportARL3 GYP1 YOR070C 3 SL Vesicular transportARL3 VAM3 YOR106W 1 SS Vesicular transportARL3 VPS17 YOR132W 1 SL Vesicular transportGYP1 CSS2 YBR036C 1 SS Small molecule transportGYP1 VMA2 YBR127C 1 SL Vacuole organization and biogenesisGYP1 ARL1 YBR164C 1 SL Vesicular transportGYP1 VPS61 YDR136C 1 SL Vesicular transport

Page 47: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

GYP1 NBP2 YDR162C 1 SS Cell polarityGYP1 SUM1 YDR310C 1 SS Chromatin/chromosome structureGYP1 ERD1 YDR414C 1 SS Protein modificationGYP1 RMD7 YER083C 1 SL Cell wall organization and biogenesisGYP1 COG7 YGL005C 1 SL Vesicular transportGYP1 CHO2 YGR157W 1 SS Lipid metabolismGYP1 GOS1 YHL031C 1 SL Vesicular transportGYP1 SYS1 YJL004C 1 SL Protein translocationGYP1 MNN11 YJL183W 1 SS Protein modificationGYP1 CPR7 YJR032W 1 SL Protein foldingGYP1 CBF1 YJR060W 1 SL Chromatin/chromosome structureGYP1 RIC1 YLR039C 1 SL Vesicular transportGYP1 VPS63 YLR261C 1 SL Vacuolar organization and biogenesisGYP1 YPT6 YLR262C 1 SL Vesicular transportGYP1 SEC22 YLR268W 1 SS Vesicular transportGYP1 COG8 YML071C 1 SL Vesicular transportGYP1 SCS7 YMR272C 1 SS Lipid metabolismGYP1 COG6 YNL041C 1 SL Vesicular transportGYP1 COG5 YNL051W 1 SL Vesicular transportGYP1 RUD3 YOR216C 1 SS Vesicular transportGYP1 ARL3 YPL051W 1 SL Vesicular transportGYP1 LGE1 YPL055C 1 SS Cell cycle controlGYP1 SUR1 YPL057C 1 SS Lipid metabolismGYP1 VMA13 YPR036W 1 SL Vacuolar organization and biogenesisRIC1 VPS8 YAL002W 0 SL Vesicular transportRIC1 SWC1 YAL011W 0 SL UnknownRIC1 FUN30 YAL019W 0 SL UnknownRIC1 PMT2 YAL023C 2 SS Protein modificationRIC1 DRS2 YAL026C 3 SS Vesicular transportRIC1 BUD14 YAR014C 0 SL Cell polarityRIC1 FUI1 YBL042C 0 SS Small molecule transportRIC1 SFT2 YBL102W 0 SS Vesicular transportRIC1 ARL1 YBR164C 0 SS Vesicular transportRIC1 RER1 YCL001W 0 SS Vesicular transportRIC1 SRO9 YCL037C 2 SL Protein synthesisRIC1 MAK31 YCR020C-A 3 SL Protein modificationRIC1 PER1 YCR044C 1 SS Other metabolismRIC1 PTC1 YDL006W 0 SL Signal transductionRIC1 BRE1 YDL074C 3 SL Chromatin/chromosome stuctureRIC1 VAM6 YDL077C 0 SS Vesicular transportRIC1 ARR4 YDL100C 0 SS Small molecule transportRIC1 RPL35A YDL191W 0 SL Protein synthesisRIC1 VPS41 YDR080W 1 SL Vesicular transportRIC1 YDR107C YDR107C 0 SS TransportRIC1 GSS1 YDR108W 3 SL Vesicular transportRIC1 ENT5 YDR153C 0 SL Vesicular transportRIC1 NBP2 YDR162C 0 SL Cell polarityRIC1 RAV2 YDR202C 0 SS Small molecule transportRIC1 YDR203W YDR203W 0 SL UnknownRIC1 UME6 YDR207C 0 SL MeiosisRIC1 SWA2 YDR320C 0 SL Vesicular transportRIC1 SWR1 YDR334W 0 SL UnknownRIC1 VPS74 YDR372C 1 SS Vacuolar organization and biogenesisRIC1 SPF1 YEL031W 0 SS Small molecule transportRIC1 YEL043W YEL043W 0 SL UnknownRIC1 VMA8 YEL051W 0 SL Vacuolar organization and biogenesisRIC1 MAK10 YEL053C 3 SL Protein modificationRIC1 RMD7 YER083C 1 SL Cell wall organization and biogenesisRIC1 YER084W YER084W 0 SL UnknownRIC1 SCS2 YER120W 1 SL Lipid metabolismRIC1 GLO3 YER122C 0 SL Vesicular transport

Page 48: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

RIC1 RAD4 YER162C 0 SS DNA repairRIC1 BST1 YFL025C 0 SS Vesicular transportRIC1 RIM15 YFL033C 0 SL MeiosisRIC1 RPL2A YFR031C-A 3 SL Protein synthesisRIC1 COG7 YGL005C 2 SL Vesicular transportRIC1 SWF3 YGL020C 3 SL UnknownRIC1 ERV14 YGL054C 2 SL Vesicular transportRIC1 GUP1 YGL084C 0 SS Lipid metabolismRIC1 SNF4 YGL115W 0 SS Protein modificationRIC1 KEM1 YGL173C 2 SL RNA processingRIC1 RTF1 YGL244W 0 SL Pol II transcriptionRIC1 UPF3 YGR072W 3 SS RNA turnoverRIC1 VMA21 YGR105W 0 SL Vacuolar organization and biogenesisRIC1 SMI1 YGR229C 0 SS Cell wall organization and biogenesisRIC1 APL6 YGR261C 2 SS Vesicular transportRIC1 GOS1 YHL031C 3 SL Vesicular transportRIC1 NEM1 YHR004C 0 SS UnknownRIC1 VPS29 YHR012W 3 SL Vesicular transportRIC1 VMA22 YHR060W 0 SL Vacuolar organization and biogenesisRIC1 YIL039W YIL039W 1 SL UnknownRIC1 SEC28 YIL076W 0 SL Vesicular transportRIC1 SYS1 YJL004C 1 SS Protein translocationRIC1 VPS35 YJL154C 0 SS Vesicular transportRIC1 RAV1 YJR033C 0 SS Vacuolar organization and biogenesisRIC1 GEF1 YJR040W 0 SS Small molecule transportRIC1 CBF1 YJR060W 1 SL Chromatin/chromosome structureRIC1 OPI3 YJR073C 0 SS Lipid metabolismRIC1 TEF4 YKL081W 0 SL Protein synthesisRIC1 CNB1 YKL190W 0 SS Cell wall organization and biogenesisRIC1 VPS1 YKR001C 0 SL Vesicular transportRIC1 VPS67 YKR020W 0 SL Vacuolar organization and biogenesisRIC1 GMH1 YKR030W 3 SL UnknownRIC1 RPL40B YKR094C 0 SL Protein synthesisRIC1 ENT4 YLL038C 0 SS Vesicular transportRIC1 VPS13 YLL040C 0 SS Vesicular transportRIC1 BRE2 YLR015W 0 SL Chromatin/chromosome structureRIC1 EMP70 YLR083C 0 SS TransportRIC1 ARP6 YLR085C 0 SL Cell structureRIC1 CSF1 YLR087C 0 SL Cell stressRIC1 IMH1 YLR309C 3 SL Vesicular transportRIC1 EST2 YLR318W 1 SL Chromatin/chromosome structureRIC1 VPS38 YLR360W 3 SL Vesicular transportRIC1 DCR2 YLR361C 1 SL UnknownRIC1 YPT7 YML001W 0 SL Vesicular transportRIC1 YMD8 YML038C 0 SL Small molecule transportRIC1 VPS71 YML041C 0 SL Vesicular transportRIC1 COG8 YML071C 2 SL Vesicular transportRIC1 MVP1 YMR004W 3 SL Vesicular transportRIC1 YMR010W YMR010W 0 SL MeiosisRIC1 STV1 YMR054W 0 SS Vacuolar organization and biogenesisRIC1 PKR1 YMR123W 3 SL UnknownRIC1 SKY1 YMR216C 2 SS RNA splicingRIC1 SCS7 YMR272C 0 SL Lipid metabolismRIC1 RCE1 YMR274C 2 SS Protein modificationRIC1 GAS1 YMR307W 3 SS Cell wall organization and biogenesisRIC1 COG6 YNL041C 3 SL Vesicular transportRIC1 COG5 YNL051W 3 SL Vesicular transportRIC1 RPL16B YNL069C 0 SL Protein synthesisRIC1 FAR11 YNL127W 1 SS UnknownRIC1 YNL136W YNL136W 0 SL UnknownRIC1 PSD1 YNL169C 0 SL Lipid metabolism

Page 49: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

RIC1 KEX2 YNL238W 0 SL Protein modificationRIC1 MID1 YNL291C 0 SL Small molecule transportRIC1 KRE25 YNL296W 3 SL UnknownRIC1 MON2 YNL297C 3 SL Vacuolar organization and biogenesisRIC1 TRF5 YNL299W 0 SL Chromatin/chromosome structureRIC1 PPG1 YNR032W 1 SL Carbohydrate metabolismRIC1 BRE5 YNR051C 0 SL UnknownRIC1 HTZ1 YOL012C 0 SL Chromatin/chromosome structureRIC1 ESC8 YOL017W 0 SS UnknownRIC1 TLG2 YOL018C 3 SL Vesicular transportRIC1 VAM10 YOR068C 1 SL Vacuolar organization and biogenesisRIC1 VPS5 YOR069W 2 SL Vesicular transportRIC1 GYP1 YOR070C 3 SL Vesicular transportRIC1 VPS21 YOR089C 0 SS Vesicular transportRIC1 INP53 YOR109W 0 SL Lipid metabolismRIC1 YOR112W YOR112W 0 SL UnknownRIC1 RGA1 YOR127W 1 SS Cell polarityRIC1 VPS17 YOR132W 3 SL Vesicular transportRIC1 RUD3 YOR216C 2 SL Vesicular transportRIC1 SNC2 YOR327C 0 SS Vesicular transportRIC1 EGD1 YPL037C 0 SL Protein foldingRIC1 ARL3 YPL051W 3 SL Vesicular transportRIC1 LGE1 YPL055C 3 SL Cell cycle controlRIC1 YPL105C YPL105C 0 SL UnknownRIC1 VPS30 YPL120W 3 SL Vesicular transportRIC1 BEM4 YPL161C 0 SL Cell polarityRIC1 APL5 YPL195W 0 SS Vesicular transportRIC1 OXR1 YPL196W 0 SS UnknownRIC1 TFP3 YPL234C 2 SL Vacuolar organization and biogenesisRIC1 DSS4 YPR017C 0 SS Vesicular transportRIC1 SRO7 YPR032W 0 SS Vesicular transportRIC1 YPR050C YPR050C 3 SL UnknownRIC1 MAK3 YPR051W 3 SL Protein modificationRIC1 MRL1 YPR079W 0 SS Vacuolar organization and biogenesisRIC1 YPR084W YPR084W 0 SL UnknownRIC1 YPR197C YPR197C 0 SL UnknownYPT6 VPS8 YAL002W 2 SL Vesicular transportYPT6 SWC1 YAL011W 0 SL UnknownYPT6 FUN30 YAL019W 3 SL UnknownYPT6 BUD14 YAR014C 2 SL Cell polarityYPT6 YBL083C YBL083C 1 SS UnknownYPT6 SFT2 YBL102W 3 SL Vesicular transportYPT6 ARL1 YBR164C 3 SL Vesicular transportYPT6 APM3 YBR288C 1 SL Vesicular transportYPT6 RER1 YCL001W 3 SL Vesicular transportYPT6 SRO9 YCL037C 0 SL Protein synthesisYPT6 MAK31 YCR020C-A 3 SL Protein modificationYPT6 PER1 YCR044C 0 SS Other metabolismYPT6 RAD18 YCR066W 1 SL DNA repairYPT6 PTC1 YDL006W 1 SS Signal transductionYPT6 BRE1 YDL074C 3 SL Chromatin/chromosome stuctureYPT6 VAM6 YDL077C 0 SS Vesicular transportYPT6 ARR4 YDL100C 1 SL Small molecule transportYPT6 RPL35A YDL191W 2 SS Protein synthesisYPT6 VPS41 YDR080W 0 SL Vesicular transportYPT6 YDR107C YDR107C 1 SL TransportYPT6 GSS1 YDR108W 3 SL Vesicular transportYPT6 SWF1 YDR126W 2 SL UnknownYPT6 ENT5 YDR153C 3 SL Vesicular transportYPT6 NBP2 YDR162C 3 SL Cell polarityYPT6 RAV2 YDR202C 2 SL Small molecule transport

Page 50: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

YPT6 YDR203W YDR203W 3 SL UnknownYPT6 SUM1 YDR310C 2 SL Chromatin/chromosome structureYPT6 SWA2 YDR320C 3 SL Vesicular transportYPT6 SWR1 YDR334W 0 SL UnknownYPT6 VID21 YDR359C 0 SS UnknownYPT6 VPS74 YDR372C 0 SL Vacuolar organization and biogenesisYPT6 YEL043W YEL043W 1 SL UnknownYPT6 VMA8 YEL051W 0 SL Vacuolar organization and biogenesisYPT6 MAK10 YEL053C 3 SL Protein modificationYPT6 YER084W YER084W 3 SL UnknownYPT6 SBH1 YER087C-A 0 SS Protein translocationYPT6 SCS2 YER120W 1 SL Lipid metabolismYPT6 GLO3 YER122C 0 SL Vesicular transportYPT6 RAD4 YER162C 0 SL DNA repairYPT6 BST1 YFL025C 3 SS Vesicular transportYPT6 RIM15 YFL033C 1 SL MeiosisYPT6 RPL2A YFR031C-A 2 SL Protein synthesisYPT6 COG7 YGL005C 2 SL Vesicular transportYPT6 SWF3 YGL020C 3 SL UnknownYPT6 ERV14 YGL054C 3 SL Vesicular transportYPT6 GUP1 YGL084C 2 SL Lipid metabolismYPT6 SNF4 YGL115W 1 SL Protein modificationYPT6 VAM7 YGL212W 2 SL Vacuolar organization and biogenesisYPT6 RTF1 YGL244W 3 SL Pol II transcriptionYPT6 ZRT1 YGL255W 0 SS Small molecule transportYPT6 VMA7 YGR020C 2 SL Vacuolar organization and biogenesisYPT6 UPF3 YGR072W 0 SS RNA turnoverYPT6 VMA21 YGR105W 3 SL Vacuolar organization and biogenesisYPT6 SMI1 YGR229C 3 SL Cell wall organization and biogenesisYPT6 APL6 YGR261C 3 SL Vesicular transportYPT6 OPI1 YHL020C 0 SL Lipid metabolismYPT6 GOS1 YHL031C 3 SL Vesicular transportYPT6 NEM1 YHR004C 1 SL UnknownYPT6 VPS29 YHR012W 3 SL Vesicular transportYPT6 VMA10 YHR039C-B 0 SL Small molecule transportYPT6 VMA22 YHR060W 0 SL Vacuolar organization and biogenesisYPT6 YIL039W YIL039W 0 SS UnknownYPT6 SEC28 YIL076W 2 SL Vesicular transportYPT6 SYS1 YJL004C 3 SL Protein translocationYPT6 SNX4 YJL036W 1 SL Protein degradationYPT6 PEP8 YJL053W 3 SL Vesicular transportYPT6 YJL123C YJL123C 3 SL UnknownYPT6 VPS35 YJL154C 3 SL Vesicular transportYPT6 RAV1 YJR033C 3 SL Vacuolar organization and biogenesisYPT6 GEF1 YJR040W 0 SL Small molecule transportYPT6 CBF1 YJR060W 3 SL Chromatin/chromosome structureYPT6 OPI3 YJR073C 3 SS Lipid metabolismYPT6 TEF4 YKL081W 2 SL Protein synthesisYPT6 CNB1 YKL190W 0 SL Cell wall organization and biogenesisYPT6 IRS4 YKR019C 2 SL Chromatin/chromosome structureYPT6 VPS67 YKR020W 2 SL Vacuolar organization and biogenesisYPT6 GMH1 YKR030W 3 SL UnknownYPT6 ENT4 YLL038C 2 SL Vesicular transportYPT6 BRE2 YLR015W 1 SL Chromatin/chromosome structureYPT6 EMP70 YLR083C 1 SL TransportYPT6 ARP6 YLR085C 3 SL Cell structureYPT6 CSF1 YLR087C 0 SL Cell stressYPT6 IMH1 YLR309C 3 SL Vesicular transportYPT6 EST2 YLR318W 3 SL Chromatin/chromosome structureYPT6 VPS38 YLR360W 3 SS Vesicular transportYPT6 DCR2 YLR361C 0 SS Unknown

Page 51: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

YPT6 YPT7 YML001W 2 SS Vesicular transportYPT6 VPS71 YML041C 2 SS Vesicular transportYPT6 COG8 YML071C 3 SL Vesicular transportYPT6 MVP1 YMR004W 3 SL Vesicular transportYPT6 YMR010W YMR010W 2 SL MeiosisYPT6 STV1 YMR054W 0 SL Vacuolar organization and biogenesisYPT6 PKR1 YMR123W 2 SL UnknownYPT6 SKY1 YMR216C 2 SS RNA splicingYPT6 RSN1 YMR266W 1 SL UnknownYPT6 RCE1 YMR274C 3 SL Protein modificationYPT6 GAS1 YMR307W 3 SS Cell wall organization and biogenesisYPT6 COG6 YNL041C 3 SL Vesicular transportYPT6 COG5 YNL051W 3 SL Vesicular transportYPT6 RPL16B YNL069C 1 SL Protein synthesisYPT6 YNL136W YNL136W 1 SS UnknownYPT6 PSD1 YNL169C 3 SL Lipid metabolismYPT6 KRE25 YNL296W 3 SL UnknownYPT6 MON2 YNL297C 3 SL Vacuolar organization and biogenesisYPT6 PPG1 YNR032W 1 SS Carbohydrate metabolismYPT6 BRE5 YNR051C 3 SL UnknownYPT6 HTZ1 YOL012C 2 SL Chromatin/chromosome structureYPT6 ESC8 YOL017W 2 SL UnknownYPT6 TLG2 YOL018C 3 SL Vesicular transportYPT6 INO4 YOL108C 3 SS Lipid metabolismYPT6 VAM10 YOR068C 2 SL Vacuolar organization and biogenesisYPT6 VPS5 YOR069W 2 SL Vesicular transportYPT6 GYP1 YOR070C 3 SL Vesicular transportYPT6 VPS21 YOR089C 0 SL Vesicular transportYPT6 VAM3 YOR106W 0 SL Vesicular transportYPT6 INP53 YOR109W 2 SL Lipid metabolismYPT6 YOR112W YOR112W 3 SL UnknownYPT6 VPS17 YOR132W 3 SL Vesicular transportYPT6 RUD3 YOR216C 3 SL Vesicular transportYPT6 EGD1 YPL037C 2 SL Protein foldingYPT6 ARL3 YPL051W 3 SL Vesicular transportYPT6 LGE1 YPL055C 3 SL Cell cycle controlYPT6 VPS30 YPL120W 2 SL Vesicular transportYPT6 BEM4 YPL161C 0 SL Cell polarityYPT6 APL5 YPL195W 3 SL Vesicular transportYPT6 OXR1 YPL196W 3 SL UnknownYPT6 TFP3 YPL234C 2 SL Vacuolar organization and biogenesisYPT6 DSS4 YPR017C 0 SL Vesicular transportYPT6 SRO7 YPR032W 0 SS Vesicular transportYPT6 YPR050C YPR050C 2 SL UnknownYPT6 MAK3 YPR051W 3 SL Protein modificationYPT6 MRL1 YPR079W 2 SS Vacuolar organization and biogenesisYPT6 YPR084W YPR084W 1 SL UnknownYPT6 YPR197C YPR197C 2 SS UnknownCDC73 VPS8 YAL002W 1 SS Vesicular transportCDC73 SWC1 YAL011W 2 SL SL UnknownCDC73 DEP1 YAL013W 2 SL Lipid metabolismCDC73 NUP60 YAR002W 1 SL Nuclear-cytoplasmic transportCDC73 ECM8 YBR076W 1 SS Cell wall organization and biogenesisCDC73 RXT2 YBR095C 3 SL UnknownCDC73 SIF2 YBR103W 0 SL Chromatin/chromosome structureCDC73 SOY YBR194W 1 SS UnknownCDC73 HPC2 YBR215W 2 SL Pol II transcriptionCDC73 PDB1 YBR221C 0 SS Carbohydrate metabolismCDC73 AOR1 YBR231C 1 SL UnknownCDC73 SRO9 YCL037C 1 SL Protein synthesisCDC73 PAT1 YCR077C 0 SL Chromatin/chromosome structure

Page 52: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

CDC73 NHP10 YDL002C 1 SS UnknownCDC73 YDL033C YDL033C 0 SL UnknownCDC73 RGP1 YDR137W 1 SS Vesicular transportCDC73 MNN10 YDR245W 1 SS Protein modificationCDC73 RTT103 YDR289C 1 SS UnknownCDC73 SWR1 YDR334W 0 SL UnknownCDC73 MSN5 YDR335W 1 SS Nuclear-cytoplasmic transportCDC73 SEM1 YDR363W-A 0 SL Vesicular transportCDC73 XRS2 YDR369C 1 SL DNA repairCDC73 LSM6 YDR378C 1 SL RNA splicingCDC73 DOT1 YDR440W 1 SL Chromatin/chromosome stuctureCDC73 VPS72 YDR485C 2 SL Vesicular transportCDC73 VAC8 YEL013W 1 SL Vacuolar organization and biogenesisCDC73 SPF1 YEL031W 2 SL Small molecule transportCDC73 YEL033W YEL033W 1 SL DifferentiationCDC73 CIN8 YEL061C 1 SL MitosisCDC73 YER084W YER084W 0 SL UnknownCDC73 SWI4 YER111C 3 SL Cell cycle controlCDC73 GLO3 YER122C 0 SL Vesicular transportCDC73 YER139C YER139C 0 SS UnknownCDC73 SPT2 YER161C 2 SL Chromatin/chromosome stuctureCDC73 PDA1 YER178W 1 SS Mitochondrion organization and biogenesisCDC73 UBP6 YFR010W 0 SL Protein modificationCDC73 SWF3 YGL020C 3 SL UnknownCDC73 DST1 YGL043W 2 SL Pol II transcriptionCDC73 KEM1 YGL173C 1 SS RNA processingCDC73 BUD13 YGL174W 1 SL Cell polarityCDC73 VID30 YGL227W 0 SL Pol II TranscriptionCDC73 RTF1 YGL244W 0 SS Pol II transcriptionCDC73 YTA7 YGR270W 1 SS Vacuolar organization and biogenesisCDC73 GOS1 YHL031C 2 SS Vesicular transportCDC73 THP2 YHR167W 0 SL RecombinationCDC73 APQ12 YIL040W 0 SL UnknownCDC73 SEC28 YIL076W 1 SL Vesicular transportCDC73 MET18 YIL128W 1 SL Pol II TranscriptionCDC73 IST3 YIR005W 0 SL RNA splicingCDC73 LSM1 YJL124C 0 SS RNA turnoverCDC73 SET2 YJL168C 1 SL Chromatin/chromosome structureCDC73 HIR3 YJR140C 0 SL Pol II transcriptionCDC73 YKL053C-A YKL053C-A 1 SL Mitochondrion organization and biogenesisCDC73 CTK1 YKL139W 0 SL Pol II transcriptionCDC73 ELF1 YKL160W 0 SL UnknownCDC73 LST4 YKL176C 1 SL Vesicular transportCDC73 DOA1 YKL213C 1 SL Protein degradationCDC73 RTT109 YLL002W 1 SL DNA repairCDC73 RIC1 YLR039C 2 SL Vesicular transportCDC73 PET309 YLR067C 1 SS RNA metabolismCDC73 ARP6 YLR085C 2 SL Cell structureCDC73 YLR168C YLR168C 0 SL UnknownCDC73 SWI6 YLR182W 1 SS Cell cycle controlCDC73 MMR1 YLR190W 1 SL UnknownCDC73 QRI5 YLR204W 1 SL UnknownCDC73 LIP2 YLR239C 1 SS Protein modificationCDC73 YPT6 YLR262C 1 SL Vesicular transportCDC73 SEC22 YLR268W 0 SL Vesicular transportCDC73 YLR269C YLR269C 1 SL UnknownCDC73 NKP2 YLR315W 1 SS Chromatin/chromosome structureCDC73 ORM2 YLR350W 2 SL Cell wall organization and biogenesisCDC73 VID22 YLR373C 1 SL Vacuolar organization and biogenesisCDC73 IKI3 YLR384C 0 SL Pol II transcriptionCDC73 YML012C-A YML013C-A 1 SL Unknown

Page 53: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

CDC73 RAD52 YML032C 1 SS DNA repairCDC73 VPS71 YML041C 2 SL Vesicular transportCDC73 LYS7 YMR038C 1 SS Amino-acid metabolismCDC73 RIM13 YMR154C 0 SS MeiosisCDC73 MRPS8 YMR158W 1 SL Mitochondrion organization and biogenesisCDC73 SAP30 YMR263W 2 SL Chromatin/chromosome structureCDC73 RCE1 YMR274C 1 SL Protein modificationCDC73 BUL1 YMR275C 1 SS Protein degradationCDC73 SSN8 YNL025C 1 SL Pol II transcriptionCDC73 PHO23 YNL097C 0 SL Phosphate metabolismCDC73 YNL140C YNL140C 0 SL UnknownCDC73 YNL198C YNL198C 1 SL UnknownCDC73 GCR2 YNL199C 1 SL Pol II TranscriptionCDC73 IES2 YNL215W 2 SS UnknownCDC73 RIM21 YNL294C 1 SS UnknownCDC73 SIN3 YOL004W 1 SL Pol II transcriptionCDC73 HTZ1 YOL012C 1 SL Chromatin/chromosome structureCDC73 MDM38 YOL027C 0 SL Mitochondrion organization and biogenesisCDC73 THP1 YOL072W 1 SL Pol II TranscriptionCDC73 RRP6 YOR001W 1 SS RNA processingCDC73 DFG16 YOR030W 1 SS DifferentiationCDC73 HIR2 YOR038C 2 SL Pol II transcriptionCDC73 DIA2 YOR080W 1 SL DifferentiationCDC73 VPS21 YOR089C 2 SS Vesicular transportCDC73 LEO1 YOR123C 1 SL Chromatin/chromosome structureCDC73 UBP2 YOR124C 1 SS Protein modificationCDC73 RUD3 YOR216C 2 SL Vesicular transportCDC73 TIM18 YOR297C 1 SL Mitochondrion organization and biogenesisCDC73 SNU66 YOR308C 2 SL RNA splicingCDC73 PDE2 YOR360C 1 SL Signal transductionCDC73 SSN3 YPL042C 1 SL Pol II transcriptionCDC73 SUR1 YPL057C 0 SL Lipid metabolismCDC73 BTS1 YPL069C 1 SL Protein modificationCDC73 CTI6 YPL181W 3 SL Chromatin/chromosome structureCDC73 YPL182C YPL182C 2 SL UnknownCDC73 MED1 YPR070W 2 SS SS Chromatin/chromosome structureCDC73 YPR084W YPR084W 0 SL UnknownSET2 SWC1 YAL011W 0 SL Unknown Krogan, 2003SET2 DEP1 YAL013W 0 SS Lipid metabolism Krogan, 2003SET2 SIF2 YBR103W 2 SS Chromatin/chromosome structure Krogan, 2003SET2 SWD3 YBR175W 0 SS Chromatin/chromosome structure Krogan, 2003SET2 DCC1 YCL016C 1 SS Chromatin/chromosome structure Krogan, 2003SET2 SNT1 YCR033W 0 SS Chromatin/chromosome structure Krogan, 2003SET2 YDL033C YDL033C 0 SL Unknown Krogan, 2003SET2 BRE1 YDL074C 2 SL Chromatin/chromosome stucture Krogan, 2003SET2 SWR1 YDR334W 3 SS Unknown Krogan, 2003SET2 VID21 YDR359C 1 SS Unknown Krogan, 2003SET2 SDC1 YDR469W 0 SS Chromatin/chromosome structure Krogan, 2003SET2 RIM8 YGL045W 1 SS Unknown Krogan, 2003SET2 RIM8 YGL046W 1 SS Unknown Krogan, 2003SET2 SOH1 YGL127C 0 SL DNA repair Krogan, 2003SET2 RTF1 YGL244W 3 SL Pol II transcription Krogan, 2003SET2 SHY1 YGR112W 2 SS Energy generation Krogan, 2003SET2 HOS4 YIL112W 0 SS Chromatin/chromosome stucture Krogan, 2003SET2 SET3 YKR029C 0 SS Chromatin/chromosome structure Krogan, 2003SET2 BRE2 YLR015W 0 SS Chromatin/chromosome structure Krogan, 2003SET2 ARP6 YLR085C 1 SL Cell structure Krogan, 2003SET2 SEC22 YLR268W 3 SL Vesicular transport Krogan, 2003SET2 VAC14 YLR386W 2 SS Vacuolar organization and biogenesis Krogan, 2003SET2 CDC73 YLR418C 0 SL Pol II transcription Krogan, 2003SET2 VPS71 YML041C 0 SS Vesicular transport Krogan, 2003

Page 54: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

SET2 GIM5 YML094W 0 SL Cell structure Krogan, 2003SET2 MSC1 YML128C 2 SL Unknown Krogan, 2003SET2 GIM3 YNL153C 0 SL Cell structure Krogan, 2003SET2 RIM21 YNL294C 1 SS Unknown Krogan, 2003SET2 MON2 YNL297C 0 SL Vacuolar organization and biogenesis Krogan, 2003SET2 BRE5 YNR051C 0 SS Unknown Krogan, 2003SET2 HTZ1 YOL012C 1 SL Chromatin/chromosome structure Krogan, 2003SET2 VAM3 YOR106W 1 SL Vesicular transport Krogan, 2003SET2 LEO1 YOR123C 1 SS Chromatin/chromosome structure Krogan, 2003SET2 LGE1 YPL055C 3 SL Cell cycle control Krogan, 2003SET2 BEM4 YPL161C 2 SL Cell polarity Krogan, 2003SET2 YPR014C YPR014C 0 SS Unknown Krogan, 2003LIA1 SRO9 YCL037C 2 SL Protein synthesisLIA1 ARF1 YDL192W 3 SL TransportLIA1 PRB1 YEL060C 2 SS Protein degradationLIA1 RMD9 YGL107C 2 SS MeiosisLIA1 SOH1 YGL127C 2 SL DNA repairLIA1 RTF1 YGL244W 3 SS Pol II transcriptionLIA1 SRB2 YHR041C 3 SS Pol II TranscriptionLIA1 YMR269W YMR269W 3 SS UnknownLIA1 AAH1 YNL141W 3 SS Nucleotide metabolismLIA1 YOR309C YOR309C 3 SL UnknownARP1 HCM1 YCR065W 3 SS Pol II transcriptionARP1 GIM4 YEL003W 3 SS Cell structureARP1 CIN8 YEL061C 2 SS MitosisARP1 BIM1 YER016W 3 SL MitosisARP1 RPL34A YER056C-A 2 SS Protein synthesisARP1 BOI2 YER114C 3 SS Cell polarityARP1 MON1 YGL124C 1 SL UnknownARP1 KIP3 YGL216W 0 SL MitosisARP1 YGL217C YGL217C 0 SL UnknownARP1 PAC10 YGR078C 2 SS Cell structureARP1 SMI1 YGR229C 3 SS Cell wall organization and biogenesisARP1 VPS29 YHR012W 3 SS Vesicular transportARP1 YKE2 YLR200W 0 SS Cell structureARP1 CLB4 YLR210W 3 SS Cell cycle controlARP1 VID22 YLR373C 2 SS Vacuolar organization and biogenesisARP1 GIM5 YML094W 1 SS Cell structureARP1 CIK1 YMR198W 2 SL MitosisARP1 GIM3 YNL153C 3 SL Cell structureARP1 BNI1 YNL271C 0 SS Cell polarityARP1 BRE5 YNR051C 0 SS UnknownARP1 CIN1 YOR349W 0 SS Cell structureARP1 KAR9 YPL269W 3 SL MitosisARP1 KAR3 YPR141C 1 SL MitosisJNM1 LTE1 YAL024C 1 SL Cell cycle controlJNM1 HCM1 YCR065W 3 SS SS Pol II transcriptionJNM1 PAT1 YCR077C 2 SL Chromatin/chromosome structureJNM1 GIM4 YEL003W 1 SS Cell structureJNM1 CIN8 YEL061C 1 SL MitosisJNM1 PAC2 YER007W 0 SS Cell structureJNM1 BIM1 YER016W 3 SL MitosisJNM1 BOI2 YER114C 3 SS SS Cell polarityJNM1 KIP3 YGL216W 3 SL MitosisJNM1 YGL217C YGL217C 3 SL UnknownJNM1 PAC10 YGR078C 0 SL Cell structureJNM1 SMI1 YGR229C 3 SS Cell wall organization and biogenesisJNM1 VPS35 YJL154C 1 SL Vesicular transportJNM1 CAP1 YKL007W 0 SS SS Cell structureJNM1 YKE2 YLR200W 0 SS Cell structureJNM1 CLB4 YLR210W 3 SL Cell cycle control

Page 55: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

JNM1 CPR6 YLR216C 2 SL Protein foldingJNM1 YLR217W YLR217W 0 SL UnknownJNM1 GIM5 YML094W 1 SL Cell structureJNM1 TUB3 YML124C 0 SS Cell structureJNM1 RPL16B YNL069C 1 SL Protein synthesisJNM1 GIM3 YNL153C 3 SS Cell structureJNM1 BNI1 YNL271C 2 SL Cell polarityJNM1 CIN1 YOR349W 0 SS SL Cell structureJNM1 CIN2 YPL241C 3 SS Cell structureJNM1 KAR9 YPL269W 3 SL MitosisJNM1 KAR3 YPR141C 0 SL MitosisNIP100 DEP1 YAL013W 3 SL Lipid metabolismNIP100 CRD1 YDL142C 0 SS SS Mitochondrion organization and biogenesisNIP100 MRPL1 YDR116C 0 SL SS Mitochondrion organization and biogenesisNIP100 EMI1 YDR512C 2 SS MeiosisNIP100 GIM4 YEL003W 1 SS Cell structureNIP100 CIN8 YEL061C 0 SL MitosisNIP100 PAC2 YER007W 0 SS Cell structureNIP100 BIM1 YER016W 3 SL MitosisNIP100 BOI2 YER114C 2 SS SS Cell polarityNIP100 MON1 YGL124C 1 SL UnknownNIP100 KIP3 YGL216W 2 SL MitosisNIP100 YGL217C YGL217C 2 SL UnknownNIP100 PAC10 YGR078C 1 SL Cell structureNIP100 CAP2 YIL034C 1 SS Cell structureNIP100 CAP1 YKL007W 3 SS Cell structureNIP100 BRE2 YLR015W 1 SS SS Chromatin/chromosome structureNIP100 YKE2 YLR200W 0 SL Cell structureNIP100 CLB4 YLR210W 2 SS SS Cell cycle controlNIP100 CPR6 YLR216C 2 SS SS Protein foldingNIP100 YLR217W YLR217W 2 SS SS UnknownNIP100 ATP10 YLR393W 3 SS SS Energy generationNIP100 GIM5 YML094W 0 SL Cell structureNIP100 CIN4 YMR138W 0 SS Cell structureNIP100 SAP30 YMR263W 1 SS SS Chromatin/chromosome structureNIP100 GAS1 YMR307W 0 SS Cell wall organization and biogenesisNIP100 GIM3 YNL153C 2 SL Cell structureNIP100 BNI1 YNL271C 2 SL Cell polarityNIP100 MCK1 YNL307C 2 SS MeiosisNIP100 CIN1 YOR349W 3 SL Cell structureNIP100 YPL205C YPL205C 1 SS MeiosisNIP100 CIN2 YPL241C 3 SL Cell structureNIP100 KAR9 YPL269W 3 SL MitosisNIP100 KAR3 YPR141C 3 SL MitosisDYN1 LTE1 YAL024C 0 SS Cell cycle controlDYN1 HCM1 YCR065W 0 SS Pol II transcriptionDYN1 GIM4 YEL003W 0 SS Cell structureDYN1 CIN8 YEL061C 0 SL MitosisDYN1 BIM1 YER016W 2 SL MitosisDYN1 BOI2 YER114C 0 SS Cell polarityDYN1 MON1 YGL124C 0 SL SL UnknownDYN1 KIP3 YGL216W 3 SL MitosisDYN1 YGL217C YGL217C 3 SL UnknownDYN1 PAC10 YGR078C 0 SL SS Cell structureDYN1 YKE2 YLR200W 0 SS Cell structureDYN1 GIM5 YML094W 0 SS SS Cell structureDYN1 GIM3 YNL153C 2 SL Cell structureDYN1 BNI1 YNL271C 0 SL Cell polarityDYN1 CIN1 YOR349W 0 SS Cell structureDYN1 KAR9 YPL269W 2 SL MitosisDYN1 KAR3 YPR141C 0 SL Mitosis

Page 56: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

DYN2 GIM4 YEL003W 0 SS Cell structureDYN2 CIN8 YEL061C 1 SL MitosisDYN2 BIM1 YER016W 1 SL MitosisDYN2 MON1 YGL124C 1 SS UnknownDYN2 KIP3 YGL216W 2 SL MitosisDYN2 YGL217C YGL217C 3 SS UnknownDYN2 PAC10 YGR078C 1 SL Cell structureDYN2 YKE2 YLR200W 0 SS Cell structureDYN2 GIM5 YML094W 0 SS Cell structureDYN2 GIM3 YNL153C 3 SL Cell structureDYN2 BNI1 YNL271C 0 SL Cell polarityDYN2 CIN1 YOR349W 0 SS Cell structureDYN2 KAR9 YPL269W 0 SS MitosisPAC11 GIM4 YEL003W 1 SS Cell structurePAC11 CIN8 YEL061C 0 SL MitosisPAC11 BIM1 YER016W 2 SL MitosisPAC11 BOI2 YER114C 0 SS Cell polarityPAC11 KIP3 YGL216W 0 SL MitosisPAC11 YGL217C YGL217C 3 SL UnknownPAC11 PAC10 YGR078C 0 SL Cell structurePAC11 YKE2 YLR200W 0 SL Cell structurePAC11 CLB4 YLR210W 1 SS Cell cycle controlPAC11 GIM5 YML094W 1 SS Cell structurePAC11 GIM3 YNL153C 2 SL Cell structurePAC11 BNI1 YNL271C 0 SL Cell polarityPAC11 CIN1 YOR349W 0 SL Cell structurePAC11 KAR9 YPL269W 2 SL MitosisYMR299c GIM4 YEL003W 1 SS Cell structureYMR299c CIN8 YEL061C 1 SL MitosisYMR299c PAC2 YER007W 1 SS Cell structureYMR299c BIM1 YER016W 1 SL MitosisYMR299c MON1 YGL124C 1 SS UnknownYMR299c KIP3 YGL216W 1 SS MitosisYMR299c YGL217C YGL217C 1 SS UnknownYMR299c PAC10 YGR078C 1 SS Cell structureYMR299c YKE2 YLR200W 1 SS Cell structureYMR299c CLB4 YLR210W 1 SS Cell cycle controlYMR299c GIM5 YML094W 1 SL Cell structureYMR299c GIM3 YNL153C 1 SL Cell structureYMR299c BNI1 YNL271C 1 SS Cell polarityYMR299c CIN1 YOR349W 1 SS Cell structureYMR299c CIN2 YPL241C 1 SS Cell structureYMR299c KAR9 YPL269W 1 SS MitosisYMR299c KAR3 YPR141C 1 SS MitosisPAC1 GIM4 YEL003W 1 SL Cell structurePAC1 CIN8 YEL061C 1 SL MitosisPAC1 BIM1 YER016W 3 SL MitosisPAC1 BEM2 YER155C 3 SL Cell polarityPAC1 FAB1 YFR019W 3 SL Lipid metabolismPAC1 KIP3 YGL216W 3 SS MitosisPAC1 YGL217C YGL217C 3 SS UnknownPAC1 PAC10 YGR078C 1 SL Cell structurePAC1 YHR168W YHR168W 1 SS UnknownPAC1 CAP1 YKL007W 3 SS Cell structurePAC1 YKE2 YLR200W 1 SS Cell structurePAC1 GIM5 YML094W 1 SL Cell structurePAC1 GIM3 YNL153C 3 SL Cell structurePAC1 BNI1 YNL271C 3 SL Cell polarityPAC1 YOR296W YOR296W 2 SS UnknownPAC1 YOR300W YOR300W 1 SS UnknownPAC1 KAR9 YPL269W 3 SL Mitosis

Page 57: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

PAC1 KAR3 YPR141C 2 SL MitosisNUM1 LTE1 YAL024C 1 SL Cell cycle controlNUM1 CCZ1 YBR131W 2 SL Vesicular transportNUM1 AOR1 YBR231C 0 SS UnknownNUM1 HCM1 YCR065W 3 SL Pol II transcriptionNUM1 PAT1 YCR077C 0 SL Chromatin/chromosome structureNUM1 GIM4 YEL003W 0 SS Cell structureNUM1 CIN8 YEL061C 0 SL MitosisNUM1 BIM1 YER016W 3 SL MitosisNUM1 FAB1 YFR019W 2 SL Lipid metabolismNUM1 MAD1 YGL086W 0 SS MitosisNUM1 MON1 YGL124C 2 SL UnknownNUM1 KIP3 YGL216W 0 SL MitosisNUM1 YGL217C YGL217C 3 SL UnknownNUM1 PAC10 YGR078C 0 SL Cell structureNUM1 SMI1 YGR229C 3 SS Cell wall organization and biogenesisNUM1 CAP2 YIL034C 1 SS Cell structureNUM1 VPS35 YJL154C 2 SS SS Vesicular transportNUM1 BFA1 YJR053W 0 SS MitosisNUM1 CAP1 YKL007W 1 SS Cell structureNUM1 DNM1 YLL001W 2 SS Cell structureNUM1 YKE2 YLR200W 0 SL Cell structureNUM1 CLB4 YLR210W 2 SL Cell cycle controlNUM1 CPR6 YLR216C 2 SL Protein foldingNUM1 YLR217W YLR217W 3 SS UnknownNUM1 BUD6 YLR319C 1 SS Cell polarityNUM1 YPT7 YML001W 2 SL Vesicular transportNUM1 GIM5 YML094W 3 SL Cell structureNUM1 BUB2 YMR055C 0 SS MitosisNUM1 TPM1 YNL079C 3 SS Cell structureNUM1 GIM3 YNL153C 0 SL Cell structureNUM1 BNI1 YNL271C 0 SL Cell polarityNUM1 ASE1 YOR058C 0 SL MitosisNUM1 YOR322C YOR322C 1 SS SS UnknownNUM1 CIN1 YOR349W 1 SS Cell structureNUM1 YPL205C YPL205C 1 SL SL MeiosisNUM1 KAR9 YPL269W 3 SL MitosisNUM1 KAR3 YPR141C 1 SL MitosisBFA1 BIK1 YCL029C 1 SL MitosisBFA1 GIM4 YEL003W 1 SS Cell structureBFA1 BIM1 YER016W 2 SL MitosisBFA1 PAC10 YGR078C 1 SS Cell structureBFA1 YKE2 YLR200W 0 SL Cell structureBFA1 GIM5 YML094W 1 SL Cell structureBFA1 GIM3 YNL153C 2 SL Cell structureBFA1 RAD50 YNL250W 1 SS DNA repairBFA1 BUB3 YOR026W 0 SL MitosisBFA1 KAR9 YPL269W 3 SL MitosisBFA1 CTF4 YPR135W 1 SS Chromatin/chromosome structureBFA1 KAR3 YPR141C 0 SL MitosisBIK1 RPL19B YBL027W 0 SL Protein synthesisBIK1 HCM1 YCR065W 0 SL Pol II transcriptionBIK1 PAT1 YCR077C 2 SL Chromatin/chromosome structureBIK1 RTT103 YDR289C 0 SL UnknownBIK1 YDR360W YDR360W 2 SL UnknownBIK1 GIM4 YEL003W 0 SL Cell structureBIK1 CIN8 YEL061C 0 SL MitosisBIK1 PAC2 YER007W 0 SL Cell structureBIK1 BIM1 YER016W 3 SL MitosisBIK1 SHC1 YER096W 0 SL MeiosisBIK1 FAB1 YFR019W 0 SL Lipid metabolism

Page 58: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

BIK1 RPL24A YGL031C 0 SL Protein synthesisBIK1 MAD1 YGL086W 0 SL MitosisBIK1 KEM1 YGL173C 0 SL RNA processingBIK1 PAC10 YGR078C 2 SL Cell structureBIK1 DBF2 YGR092W 3 SS Cell cycle controlBIK1 BUB1 YGR188C 0 SL MitosisBIK1 MSL1 YIR009W 0 SS RNA splicingBIK1 MAD2 YJL030W 0 SS MitosisBIK1 RPA34 YJL148W 0 SS Protein synthesisBIK1 RIC1 YLR039C 0 SS Vesicular transportBIK1 YKE2 YLR200W 0 SL Cell structureBIK1 GIM5 YML094W 2 SL Cell structureBIK1 YML095C-A YML095C-A 0 SL UnknownBIK1 TUB3 YML124C 0 SL Cell structureBIK1 BUB2 YMR055C 2 SL MitosisBIK1 CIN4 YMR138W 0 SS Cell structureBIK1 INP52 YNL106C 0 SL Lipid metabolismBIK1 GIM3 YNL153C 2 SL Cell structureBIK1 HTZ1 YOL012C 0 SL Chromatin/chromosome structureBIK1 BUB3 YOR026W 0 SL MitosisBIK1 ASE1 YOR058C 2 SL MitosisBIK1 RBL2 YOR265W 0 SS Cell structureBIK1 CIN1 YOR349W 0 SL Cell structureBIK1 CIN2 YPL241C 2 SL Cell structureBIK1 KAR9 YPL269W 3 SL MitosisARP6 DEP1 YAL013W 3 SL SL Lipid metabolismARP6 CSS2 YBR036C 0 SS Small molecule transportARP6 AKL1 YBR059C 0 SS UnknownARP6 CBP6 YBR120C 0 SS Protein synthesisARP6 SWD3 YBR175W 2 SS Chromatin/chromosome structureARP6 MRC1 YCL060C 3 SS DNA repairARP6 HCM1 YCR065W 3 SS Pol II transcriptionARP6 YDL033C YDL033C 1 SS UnknownARP6 BRE1 YDL074C 3 SL Chromatin/chromosome stuctureARP6 GSS1 YDR108W 2 SS Vesicular transportARP6 RGP1 YDR137w 0 SS Vesicular transportARP6 YDR360W YDR360W 0 SS UnknownARP6 GIM4 YEL003W 3 SL Cell structureARP6 PAC2 YER007W 1 SL Cell structureARP6 BIM1 YER016W 1 SL SL MitosisARP6 GLO3 YER122C 1 SL Vesicular transportARP6 DEG1 YFL001W 0 SL SL RNA processingARP6 MAD1 YGL086W 0 SS MitosisARP6 BUD13 YGL174W 1 SL SL Cell polarityARP6 RTF1 YGL244W 3 SL SL Pol II transcriptionARP6 YGR071C YGR071C 0 SS UnknownARP6 PAC10 YGR078C 0 SL Cell structureARP6 BUB1 YGR188C 2 SL MitosisARP6 SET2 YJL168C 3 SS Chromatin/chromosome structureARP6 MGM101 YJR144W 1 SS Energy generationARP6 BRE2 YLR015W 1 SL Chromatin/chromosome structureARP6 RIC1 YLR039C 3 SS Vesicular transportARP6 SPT8 YLR055C 2 SL Chromatin/chromosome structureARP6 PET309 YLR067C 1 SL RNA metabolismARP6 HOG1 YLR113W 0 SS Signal transductionARP6 YPT6 YLR262C 0 SS Vesicular transportARP6 SEC22 YLR268W 3 SL Vesicular transportARP6 EST2 YLR318W 3 SS Chromatin/chromosome structureARP6 YLR374C YLR374C 2 SS UnknownARP6 YML090W YML090W 3 SS UnknownARP6 GIM5 YML094W 1 SL Cell structure

Page 59: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

ARP6 TUB3 YML124C 2 SL Cell structureARP6 COG6 YNL041C 0 SS Vesicular transportARP6 PHO23 YNL097C 2 SS Phosphate metabolismARP6 GIM3 YNL153C 2 SL Cell structureARP6 KRE25 YNL296W 0 SS UnknownARP6 MET22 YOL064C 2 SL Amino-acid metabolismARP6 WHI2 YOR043W 0 SS Cell cycle controlARP6 LEO1 YOR123C 1 SS Chromatin/chromosome structureARP6 SER1 YOR184W 2 SS Amino-acid metabolismARP6 RUD3 YOR216C 2 SS Vesicular transportARP6 SNU66 YOR308C 0 SS RNA splicingARP6 CIN1 YOR349W 3 SL Cell structureARP6 LGE1 YPL055C 3 SL Cell cycle controlARP6 CTI6 YPL181W 3 SL Chromatin/chromosome structureARP6 YPL182C YPL182C 3 SL UnknownARP6 THI6 YPL214C 0 SS Other metabolismARP6 CIN2 YPL241C 2 SS Cell structureASE1 BIK1 YCL029C 3 SL MitosisASE1 CSM1 YCR086W 3 SL MeiosisASE1 FIN1 YDR130C 3 SL UnknownASE1 YDR149C YDR149C 3 SL UnknownASE1 NUM1 YDR150W 2 SL MitosisASE1 DYN2 YDR424C 3 SL MitosisASE1 PAC11 YDR488C 1 SL MitosisASE1 GIM4 YEL003W 1 SS Cell structureASE1 CIN8 YEL061C 1 SL MitosisASE1 BIM1 YER016W 2 SL MitosisASE1 BEM2 YER155C 0 SL Cell polarityASE1 PAC10 YGR078C 0 SL Cell structureASE1 ARP1 YHR129C 3 SL MitosisASE1 ELM1 YKL048C 2 SL Cell polarityASE1 DYN1 YKR054C 2 SL MitosisASE1 YLL049W YLL049W 3 SL UnknownASE1 YLR254C YLR254C 3 SL UnknownASE1 VAC14 YLR386W 1 SL Vacuolar organization and biogenesisASE1 GIM5 YML094W 0 SS Cell structureASE1 JNM1 YMR294W 3 SL MitosisASE1 YMR299C YMR299C 3 SL MitosisASE1 GIM3 YNL153C 3 SL Cell structureASE1 BNI1 YNL271C 1 SS Cell polarityASE1 PAC1 YOR269W 3 SL MitosisASE1 KIP2 YPL155C 0 SS MitosisASE1 NIP100 YPL174C 3 SL MitosisASE1 CLB2 YPR119W 1 SL Cell cycle controlASE1 KAR3 YPR141C 2 SL MitosisKAR9 BIK1 YCL029C 2 SL MitosisKAR9 YDR149C YDR149C 3 SL UnknownKAR9 NUM1 YDR150W 2 SL MitosisKAR9 DYN2 YDR424C 0 SS MitosisKAR9 PAC11 YDR488C 3 SL MitosisKAR9 GIM4 YEL003W 0 SL Cell structureKAR9 PAC10 YGR078C 1 SL Cell structureKAR9 ARP1 YHR129C 3 SL MitosisKAR9 BFA1 YJR053W 2 SL MitosisKAR9 IXR1 YKL032C 1 SS DNA repairKAR9 DYN1 YKR054C 3 SL MitosisKAR9 YLL049W YLL049W 3 SL UnknownKAR9 YKE2 YLR200W 0 SS Cell structureKAR9 GIM5 YML094W 0 SS Cell structureKAR9 BUB2 YMR055C 2 SL MitosisKAR9 JNM1 YMR294W 3 SL Mitosis

Page 60: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

KAR9 YMR299C YMR299C 0 SL MitosisKAR9 GIM3 YNL153C 0 SL Cell structureKAR9 KIN4 YOR233W 0 SS SS Protein modificationKAR9 PAC1 YOR269W 3 SL MitosisKAR9 KIP2 YPL155C 2 SL MitosisKAR9 NIP100 YPL174C 2 SL MitosisKAR9 MCM16 YPR046W 0 SS Chromatin/chromosome structureMYO2-14 SKT5 YBL061C 0 SS Cell wall organization and biogenesisMYO2-14 YBL062W YBL062W 0 SS UnknownMYO2-14 CHS3 YBR023C 0 SS Cell wall organization and biogenesisMYO2-14 BEM1 YBR200W 3 SL Cell polarityMYO2-14 BIK1 YCL029C 0 SL MitosisMYO2-14 PTC1 YDL006W 1 SL Signal transductionMYO2-14 SHS1 YDL225W 1 SL CytokinesisMYO2-14 YDR149C YDR149C 2 SL UnknownMYO2-14 NUM1 YDR150W 2 SL MitosisMYO2-14 DYN2 YDR424C 0 SS MitosisMYO2-14 PAC11 YDR488C 3 SL MitosisMYO2-14 BEM2 YER155C 2 SL Cell polarityMYO2-14 FAB1 YFR019W 3 SL Lipid metabolismMYO2-14 CKB1 YGL019W 2 SL Cell cycle controlMYO2-14 YGL211W YGL211W 0 SS UnknownMYO2-14 ELP2 YGR200C 2 SL Pol II transcriptionMYO2-14 YGR228W YGR228W 3 SS UnknownMYO2-14 SMI1 YGR229C 3 SL Cell wall organization and biogenesisMYO2-14 SLT2 YHR030C 1 SL Cell wall organization and biogenesisMYO2-14 UBA4 YHR111W 3 SS Protein modificationMYO2-14 ARP1 YHR129C 3 SL MitosisMYO2-14 CHS7 YHR142W 2 SS Cell wall organization and biogenesisMYO2-14 URM1 YIL008W 2 SL Protein modificationMYO2-14 BCK1 YJL095W 2 SL Cell wall organization and biogenesisMYO2-14 BFA1 YJR053W 2 SL MitosisMYO2-14 RPS4A YJR145C 0 SS Protein synthesisMYO2-14 ELM1 YKL048C 1 SS Cell polarityMYO2-14 DYN1 YKR054C 0 SL MitosisMYO2-14 YKR074W YKR074W 2 SL UnknownMYO2-14 YLL049W YLL049W 3 SL UnknownMYO2-14 CHS5 YLR330W 0 SS Cell wall organization and biogenesisMYO2-14 FLM1 YLR368W 2 SL Mitochondrion organization and biogenesisMYO2-14 VAC14 YLR386W 3 SS Vacuolar organization and biogenesisMYO2-14 BUB2 YMR055C 1 SS MitosisMYO2-14 TPM1 YNL079C 3 SL Cell structureMYO2-14 YNL119W YNL119W 2 SL SL UnknownMYO2-14 YNL120C YNL120C 2 SL UnknownMYO2-14 BNI4 YNL233W 2 SS CytokinesisMYO2-14 CLA4 YNL298W 2 SL Cell polarityMYO2-14 CKB2 YOR039W 0 SL Cell cycle controlMYO2-14 PAC1 YOR269W 3 SL MitosisMYO2-14 ELP3 YPL086C 3 SL Pol II transcriptionMYO2-14 ELP4 YPL101W 2 SL Pol II transcriptionMYO2-14 KIP2 YPL155C 2 SL MitosisMYO2-14 NIP100 YPL174C 0 SL MitosisCLB4 NUM1 YDR150W 1 SS MitosisCLB4 PAC11 YDR488C 1 SS MitosisCLB4 PAC10 YGR078C 0 SS Cell structureCLB4 ARP1 YHR129C 2 SS MitosisCLB4 YLL049W YLL049W 2 SS UnknownCLB4 CTF18 YMR078C 0 SS Chromatin/chromosome structureCLB4 JNM1 YMR294W 3 SS MitosisCLB4 YMR299C YMR299C 0 SS MitosisCLB4 NIP100 YPL174C 3 SS Mitosis

Page 61: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

CLB4 KAR3 YPR141C 2 SL MitosisKIP2 DRS2 YAL026C 2 SL Vesicular transportKIP2 GIM4 YEL003W 1 SL Cell structureKIP2 CIN8 YEL061C 2 SL MitosisKIP2 PAC2 YER007W 1 SS SS Cell structureKIP2 BIM1 YER016W 3 SL MitosisKIP2 PAC10 YGR078C 1 SL Cell structureKIP2 DBF2 YGR092W 0 SL Cell cycle controlKIP2 YKE2 YLR200W 1 SL Cell structureKIP2 GIM5 YML094W 1 SL Cell structureKIP2 TUB3 YML124C 0 SL Cell structureKIP2 GIM3 YNL153C 2 SL Cell structureKIP2 ASE1 YOR058C 1 SS SL MitosisKIP2 CIN1 YOR349W 0 SS SS Cell structureKIP2 CIN2 YPL241C 1 SS SS Cell structureKIP2 KAR9 YPL269W 0 SL MitosisKIP3 SHE1 YBL031W 2 SL UnknownKIP3 DCC1 YCL016C 1 SS Chromatin/chromosome structureKIP3 YDR149C YDR149C 3 SL UnknownKIP3 NUM1 YDR150W 3 SL MitosisKIP3 DYN2 YDR424C 3 SL MitosisKIP3 PAC11 YDR488C 3 SL MitosisKIP3 BIM1 YER016W 2 SL MitosisKIP3 YGL152C YGL152C 3 SS UnknownKIP3 KEM1 YGL173C 0 SS RNA processingKIP3 ARP1 YHR129C 3 SL MitosisKIP3 CTF8 YHR191C 0 SS Chromatin/chromosome structureKIP3 DYN1 YKR054C 3 SL MitosisKIP3 YLL049W YLL049W 2 SL UnknownKIP3 CTF18 YMR078C 0 SL Chromatin/chromosome structureKIP3 JNM1 YMR294W 2 SL MitosisKIP3 YMR299C YMR299C 3 SL MitosisKIP3 SLK19 YOR195W 1 SS Chromatin/chromosome structureKIP3 PAC1 YOR269W 3 SL MitosisKIP3 NIP100 YPL174C 3 SL MitosisKIP3 CTF4 YPR135W 1 SS Chromatin/chromosome structureKIP3 KAR3 YPR141C 0 SL MitosisCIN8 KIP1 YBL063W 2 SL MitosisCIN8 IML3 YBR107C 0 SS Chromatin/chromosome structureCIN8 MRPL36 YBR122C 3 SL Protein synthesisCIN8 DCC1 YCL016C 3 SS SL Chromatin/chromosome structureCIN8 BIK1 YCL029C 2 SS SL MitosisCIN8 CSM1 YCR086W 2 SL MeiosisCIN8 YDR149C YDR149C 0 SL UnknownCIN8 NUM1 YDR150W 0 SL MitosisCIN8 CHL4 YDR254W 1 SS Chromatin/chromosome structureCIN8 MCM21 YDR318W 1 SS SL Chromatin/chromosome structureCIN8 DYN2 YDR424C 3 SL MitosisCIN8 PPM1 YDR435C 2 SS Protein modificationCIN8 PAC11 YDR488C 2 SL MitosisCIN8 GIM4 YEL003W 1 SS Cell structureCIN8 PAC2 YER007W 0 SS Cell structureCIN8 BIM1 YER016W 0 SS MitosisCIN8 BEM2 YER155C 2 SL Cell polarityCIN8 BMH1 YER177W 1 SL DifferentiationCIN8 MAD1 YGL086W 2 SL MitosisCIN8 HUR1 YGL168W 0 SL UnknownCIN8 PAC10 YGR078C 0 SL Cell structureCIN8 BUB1 YGR188C 2 SS MitosisCIN8 SMI1 YGR229C 2 SL Cell wall organization and biogenesisCIN8 ARP1 YHR129C 2 SL Mitosis

Page 62: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

CIN8 MAD3 YJL013C 3 SL MitosisCIN8 MAD2 YJL030W 0 SL MitosisCIN8 BFA1 YJR053W 3 SL MitosisCIN8 MCM22 YJR135C 0 SS Chromatin/chromosome structureCIN8 ELM1 YKL048C 0 SL Cell polarityCIN8 DYN1 YKR054C 3 SL MitosisCIN8 YLL049W YLL049W 0 SL UnknownCIN8 YKE2 YLR200W 1 SS Cell structureCIN8 CLB4 YLR210W 1 SS Cell cycle controlCIN8 CTF3 YLR381W 0 SS Chromatin/chromosome structureCIN8 GIM5 YML094W 1 SL Cell structureCIN8 TUB3 YML124C 1 SL Cell structureCIN8 CSM3 YMR048W 1 SL MeiosisCIN8 BUB2 YMR055C 2 SL MitosisCIN8 CTF18 YMR078C 0 SL Chromatin/chromosome structureCIN8 CIN4 YMR138W 1 SL Cell structureCIN8 JNM1 YMR294W 3 SL MitosisCIN8 YMR299C YMR299C 3 SL MitosisCIN8 GIM3 YNL153C 2 SL Cell structureCIN8 TOF1 YNL273W 0 SL DNA repairCIN8 CLA4 YNL298W 0 SL Cell polarityCIN8 RTS1 YOR014W 1 SL Cell stressCIN8 SLK19 YOR195W 2 SL Chromatin/chromosome structureCIN8 RBL2 YOR265W 0 SS Cell structureCIN8 PAC1 YOR269W 3 SL MitosisCIN8 CIN1 YOR349W 2 SL Cell structureCIN8 CHL1 YPL008W 3 SL Chromatin/chromosome structureCIN8 CTF19 YPL018W 3 SL Chromatin/chromosome structureCIN8 RRD2 YPL152W 3 SL UnknownCIN8 KIP2 YPL155C 2 SL MitosisCIN8 NIP100 YPL174C 0 SL MitosisCIN8 CIN2 YPL241C 1 SL Cell structureCIN8 MCM16 YPR046W 1 SL Chromatin/chromosome structureCIN8 CLB2 YPR119W 3 SL Cell cycle controlCIN8 CTF4 YPR135W 0 SS Chromatin/chromosome structureKAR3 LTE1 YAL024C 2 SL Cell cycle controlKAR3 NUP60 YAR002W 2 SL Nuclear-cytoplasmic transportKAR3 BUD14 YAR014C 2 SL Cell polarityKAR3 MUM2 YBR057C 0 SL MeiosisKAR3 SIF2 YBR103W 2 SL Chromatin/chromosome structureKAR3 IML3 YBR107C 3 SL Chromatin/chromosome structureKAR3 MRC1 YCL061C 0 SL DNA repairKAR3 RAD61 YDR014W 3 SL UnknownKAR3 NUM1 YDR150W 2 SL MitosisKAR3 CHL4 YDR254W 3 SL Chromatin/chromosome structureKAR3 SWM1 YDR260C 0 SL MeiosisKAR3 MCM21 YDR318W 2 SL Chromatin/chromosome structureKAR3 SEM1 YDR363W-A 3 SL Vesicular transportKAR3 XRS2 YDR369C 0 SL DNA repairKAR3 PAC11 YDR488C 0 SL MitosisKAR3 GIM4 YEL003W 0 SL Cell structureKAR3 BEM2 YER155C 3 SL Cell polarityKAR3 BMH1 YER177W 2 SL DifferentiationKAR3 UBP6 YFR010W 2 SL Protein modificationKAR3 CDC26 YFR036W 0 SL Cell cycle controlKAR3 MAD1 YGL086W 3 SL MitosisKAR3 PMR1 YGL167C 3 SL Small molecule transportKAR3 HUR1 YGL168W 3 SL UnknownKAR3 KEM1 YGL173C 3 SL RNA processingKAR3 KIP3 YGL216W 3 SL MitosisKAR3 PAC10 YGR078C 2 SL Cell structure

Page 63: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

KAR3 DBF2 YGR092W 2 SL Cell cycle controlKAR3 PRE9 YGR135W 3 SL Protein degradationKAR3 BUB1 YGR188C 2 SL MitosisKAR3 ARD1 YHR013C 0 SL Chromatin/chromosome structureKAR3 ARP1 YHR129C 2 SL MitosisKAR3 CTF8 YHR191C 2 SL Chromatin/chromosome structureKAR3 YHR194W YHR194W 2 SL Mitochondrion organization and biogenesisKAR3 RPN10 YHR200W 2 SL Pol II transcriptionKAR3 YIL090W YIL090W 2 SL UnknownKAR3 MAD3 YJL013C 3 SL MitosisKAR3 MAD2 YJL030W 3 SL MitosisKAR3 ASF1 YJL115W 2 SL Chromatin/chromosome structureKAR3 SOD1 YJR104C 0 SL Cell stressKAR3 MCM22 YJR135C 3 SL Chromatin/chromosome structureKAR3 DYN1 YKR054C 2 SL MitosisKAR3 RTT109 YLL002W 2 SL DNA repairKAR3 YLL049W YLL049W 2 SL UnknownKAR3 ARP6 YLR085C 0 SS Cell structureKAR3 YKE2 YLR200W 3 SL Cell structureKAR3 CLB4 YLR210W 2 SL Cell cycle controlKAR3 CPR6 YLR216C 3 SL Protein foldingKAR3 YLR217W YLR217W 3 SL UnknownKAR3 CTF3 YLR381W 3 SL Chromatin/chromosome structureKAR3 RAD52 YML032C 2 SL DNA repairKAR3 GIM5 YML094W 2 SL Cell structureKAR3 CSM3 YMR048W 3 SL MeiosisKAR3 BUB2 YMR055C 0 SL MitosisKAR3 JNM1 YMR294W 3 SL MitosisKAR3 GIM3 YNL153C 3 SL Cell structureKAR3 TOF1 YNL273W 3 SL DNA repairKAR3 MCK1 YNL307C 3 SL MeiosisKAR3 PSH1 YOL054W 2 SL Cell stressKAR3 BUB3 YOR026W 2 SL MitosisKAR3 ASE1 YOR058C 2 SL MitosisKAR3 SLK19 YOR195W 3 SL Chromatin/chromosome structureKAR3 PAC1 YOR269W 0 SL MitosisKAR3 CHL1 YPL008W 3 SL Chromatin/chromosome structureKAR3 CTF19 YPL018W 3 SL Chromatin/chromosome structureKAR3 RRD2 YPL152W 3 SL UnknownKAR3 NIP100 YPL174C 0 SL MitosisKAR3 MCM16 YPR046W 3 SL Chromatin/chromosome structureYDR332w SHP1 YBL058W 0 SS Carbohydrate metabolismYDR332w HHF1 YBR009C 3 SL Chromatin/chromosome structureYDR332w RAD61 YDR014W 3 SL UnknownYDR332w HTA1 YDR225W 0 SL Chromatin/chromosome structureYDR332w PEX5 YDR244W 2 SS Lipid metabolismYDR332w PEX10 YDR265W 2 SS Peroxisome organization and biogenesisYDR332w BIM1 YER016W 3 SL MitosisYDR332w HOP2 YGL033W 0 SS MeiosisYDR332w MAD1 YGL086W 3 SL MitosisYDR332w UBR1 YGR184C 2 SS Protein degradationYDR332w BUB1 YGR188C 2 SL MitosisYDR332w CTF8 YHR191C 0 SL Chromatin/chromosome structureYDR332w MAD3 YJL013C 0 SL MitosisYDR332w MAD2 YJL030W 3 SL MitosisYDR332w GIM5 YML094W 0 SL Cell structureYDR332w YML095C-A YML095C-A 0 SL UnknownYDR332w CIK1 YMR198W 2 SL MitosisYDR332w INP52 YNL106C 3 SS Lipid metabolismYDR332w GIM3 YNL153C 0 SL Cell structureYDR332w HTZ1 YOL012C 0 SS Chromatin/chromosome structure

Page 64: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

YDR332w BUB3 YOR026W 0 SS MitosisYDR332w CHL1 YPL008W 3 SL Chromatin/chromosome structureYDR332w CTF4 YPR135W 2 SL Chromatin/chromosome structureYDR332w KAR3 YPR141C 0 SL MitosisTUB3 SWC1 YAL011W 2 SL UnknownTUB3 BIK1 YCL029C 0 SL MitosisTUB3 GIM4 YEL003W 2 SL Cell structureTUB3 CIN8 YEL061C 1 SL MitosisTUB3 PAC2 YER007W 2 SL Cell structureTUB3 MAD1 YGL086W 0 SL MitosisTUB3 PAC10 YGR078C 2 SL Cell structureTUB3 ARP1 YHR129C 0 SS MitosisTUB3 MAD3 YJL013C 0 SL MitosisTUB3 YKE2 YLR200W 0 SL Cell structureTUB3 VPS71 YML041C 2 SL Vesicular transportTUB3 GIM5 YML094W 1 SS Cell structureTUB3 CIN4 YMR138W 0 SS Cell structureTUB3 GIM3 YNL153C 3 SL Cell structureTUB3 HTZ1 YOL012C 2 SL Chromatin/chromosome structureTUB3 DSE3 YOR264W 2 SL DifferentiationTUB3 RBL2 YOR265W 3 SL Cell structureTUB3 PNT1 YOR266W 3 SL Mitochondrion organization and biogenesisTUB3 CIN1 YOR349W 3 SL Cell structureTUB3 NIP100 YPL174C 1 SS MitosisTUB3 CIN2 YPL241C 3 SL Cell structureRBL2 GIM4 YEL003W 1 SL Cell structureRBL2 PAC2 YER007W 0 SL Cell structureRBL2 PAC10 YGR078C 1 SL Cell structureRBL2 YKE2 YLR200W 0 SL Cell structureRBL2 GIM5 YML094W 0 SS Cell structureRBL2 TUB3 YML124C 3 SS Cell structureRBL2 CIN4 YMR138W 0 SL Cell structureRBL2 GIM3 YNL153C 0 SL Cell structureRBL2 BUB3 YOR026W 0 SL MitosisRBL2 CIN1 YOR349W 0 SS Cell structureRBL2 CIN2 YPL241C 0 SL Cell structurePAC2 BIK1 YCL029C 0 SL MitosisPAC2 MAD1 YGL086W 0 SS MitosisPAC2 PAC10 YGR078C 0 SL Cell structurePAC2 BUB1 YGR188C 0 SL MitosisPAC2 MAD2 YJL030W 0 SS MitosisPAC2 YKE2 YLR200W 0 SL Cell structurePAC2 GIM5 YML094W 1 SS Cell structurePAC2 TUB3 YML124C 2 SL Cell structurePAC2 CTF18 YMR078C 0 SL Chromatin/chromosome structurePAC2 GIM3 YNL153C 1 SL Cell structurePAC2 RBL2 YOR265W 0 SL Cell structureCIN2 BIK1 YCL029C 2 SL SL MitosisCIN2 GIM4 YEL003W 3 SL Cell structureCIN2 MAD1 YGL086W 0 SL MitosisCIN2 PAC10 YGR078C 1 SL Cell structureCIN2 BUB1 YGR188C 0 SL SL MitosisCIN2 MAD3 YJL013C 0 SS MitosisCIN2 MAD2 YJL030W 1 SL MitosisCIN2 BFA1 YJR053W 0 SL MitosisCIN2 YKE2 YLR200W 0 SS Cell structureCIN2 GIM5 YML094W 1 SS Cell structureCIN2 TUB3 YML124C 2 SL Cell structureCIN2 BUB2 YMR055C 0 SS MitosisCIN2 CTF18 YMR078C 0 SL Chromatin/chromosome structureCIN2 JNM1 YMR294W 0 SS SS Mitosis

Page 65: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

CIN2 GIM3 YNL153C 2 SL Cell structureCIN2 RBL2 YOR265W 0 SL Cell structureCIN2 CIN1 YOR349W 0 SS Cell structureCIN2 NIP100 YPL174C 2 SS SS MitosisCIN4 BIK1 YCL029C 0 SS MitosisCIN4 GIM4 YEL003W 0 SS Cell structureCIN4 CIN8 YEL061C 1 SL MitosisCIN4 PAC10 YGR078C 1 SS Cell structureCIN4 YKE2 YLR200W 0 SL Cell structureCIN4 GIM5 YML094W 0 SL Cell structureCIN4 TUB3 YML124C 0 SS Cell structureCIN4 GIM3 YNL153C 1 SS Cell structureCIN4 RBL2 YOR265W 0 SL Cell structureCIN4 CIN1 YOR349W 0 SS Cell structureCTF4 NUP60 YAR002W 0 SS Nuclear-cytoplasmic transportCTF4 SWD1 YAR003W 0 SS Chromatin/chromosome structureCTF4 SLA1 YBL007C 0 SL Cell polarityCTF4 MUM2 YBR057C 2 SL MeiosisCTF4 MMS4 YBR100W 1 SS DNA repairCTF4 IML3 YBR107C 1 SS Chromatin/chromosome structureCTF4 AOR1 YBR231C 1 SS UnknownCTF4 DCC1 YCL016C 3 SL Chromatin/chromosome structureCTF4 MRC1 YCL060C 3 SL DNA repairCTF4 MRC1 YCL061C 3 SL DNA repairCTF4 HEX3 YDL013W 1 SS MeiosisCTF4 RPN4 YDL020C 0 SL Protein degradationCTF4 CLB3 YDL155W 0 SS Cell cycle controlCTF4 SHS1 YDL225W 0 SS CytokinesisCTF4 RAD57 YDR004W 1 SS DNA repairCTF4 RAD61 YDR014W 0 SL UnknownCTF4 RAD55 YDR076W 1 SS DNA repairCTF4 HTA1 YDR225W 1 SS Chromatin/chromosome structureCTF4 CHL4 YDR254W 0 SL Chromatin/chromosome structureCTF4 PMP3 YDR276C 1 SS Small molecule transportCTF4 MCM21 YDR318W 2 SL Chromatin/chromosome structureCTF4 GIM4 YEL003W 0 SL Cell structureCTF4 RAD23 YEL037C 1 SS DNA repairCTF4 CIN8 YEL061C 0 SS MitosisCTF4 BIM1 YER016W 3 SL MitosisCTF4 ISC1 YER019W 0 SL Lipid metabolismCTF4 RMD7 YER083C 1 SS Cell wall organization and biogenesisCTF4 RAD51 YER095W 0 SL DNA repairCTF4 SLX8 YER116C 2 SL DNA repairCTF4 CHD1 YER164W 0 SS Chromatin/chromosome structureCTF4 RAD24 YER173W 1 SS DNA repairCTF4 UBP6 YFR010W 0 SL Protein modificationCTF4 CDC26 YFR036W 2 SL Cell cycle controlCTF4 SSF73 YGL066W 3 SL Pol II transcriptionCTF4 MAD1 YGL086W 3 SS MitosisCTF4 MMS2 YGL087C 0 SS DNA repairCTF4 SOH1 YGL127C 1 SS DNA repairCTF4 RAD54 YGL163C 1 SS DNA repairCTF4 HUR1 YGL168W 0 SL SL UnknownCTF4 KEM1 YGL173C 0 SL RNA processingCTF4 KIP3 YGL216W 0 SS MitosisCTF4 RTF1 YGL244W 0 SS Pol II transcriptionCTF4 PAC10 YGR078C 0 SL Cell structureCTF4 UBR1 YGR184C 3 SL Protein degradationCTF4 BUB1 YGR188C 0 SS MitosisCTF4 SMI1 YGR229C 2 SS Cell wall organization and biogenesisCTF4 ARD1 YHR013C 0 SS Chromatin/chromosome structure

Page 66: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

CTF4 RRM3 YHR031C 2 SL DNA replicationCTF4 CTF8 YHR191C 0 SL Chromatin/chromosome structureCTF4 RPN10 YHR200W 0 SL Pol II transcriptionCTF4 MAD3 YJL013C 0 SS MitosisCTF4 MAD2 YJL030W 0 SS MitosisCTF4 HPR5 YJL092W 3 SL DNA repairCTF4 POL32 YJR043C 0 SS DNA replicationCTF4 SOD1 YJR104C 0 SL Cell stressCTF4 MCM22 YJR135C 0 SL Chromatin/chromosome structureCTF4 RPS4A YJR145C 0 SS Protein synthesisCTF4 HSL1 YKL101W 2 SS Cell cycle controlCTF4 RAD27 YKL113C 2 SL DNA repairCTF4 RAD5 YLR032W 0 SL DNA repairCTF4 ARP6 YLR085C 0 SS Cell structureCTF4 STM1 YLR150W 1 SS Nucleotide metabolismCTF4 TOP3 YLR234W 0 SS Chromatin/chromosome structureCTF4 YLR235C YLR235C 0 SL UnknownCTF4 SEC22 YLR268W 0 SS Vesicular transportCTF4 CTF3 YLR381W 2 SS Chromatin/chromosome structureCTF4 TSA1 YML028W 2 SL Cell stressCTF4 RAD52 YML032C 1 SL DNA repairCTF4 GIM5 YML094W 2 SL Cell structureCTF4 LYS7 YMR038C 0 SS Amino-acid metabolismCTF4 CSM3 YMR048W 3 SL MeiosisCTF4 BUB2 YMR055C 0 SS MitosisCTF4 CTF18 YMR078C 0 SS Chromatin/chromosome structureCTF4 SGS1 YMR190C 0 SS DNA repairCTF4 MRE11 YMR224C 0 SL DNA repairCTF4 GIM3 YNL153C 0 SL Cell structureCTF4 RAD50 YNL250W 0 SL DNA repairCTF4 TOF1 YNL273W 3 SL DNA repairCTF4 MID1 YNL291C 1 SS Small molecule transportCTF4 CLA4 YNL298W 2 SL Cell polarityCTF4 MCK1 YNL307C 0 SS MeiosisCTF4 BRE5 YNR051C 0 SL UnknownCTF4 HTZ1 YOL012C 0 SS Chromatin/chromosome structureCTF4 RTS1 YOR014W 1 SL Cell stressCTF4 BUB3 YOR026W 0 SL MitosisCTF4 ELG1 YOR144C 2 SL DNA repairCTF4 SLK19 YOR195W 0 SS Chromatin/chromosome structureCTF4 YPL017C YPL017C 0 SL UnknownCTF4 CTF19 YPL018W 2 SL Chromatin/chromosome structureCTF4 NCE4 YPL024W 0 SL Cell wall organization and biogenesisCTF4 LGE1 YPL055C 2 SS Cell cycle controlCTF4 SUR1 YPL057C 3 SS Lipid metabolismCTF4 YPL144W YPL144W 3 SS SS MeiosisCTF4 DDC1 YPL194W 1 SS DNA repairCTF4 VIK1 YPL253C 1 SS MitosisCTF4 YPR015C YPR015C 0 SS Pol II TranscriptionCTF4 RLF2 YPR018W 0 SL Chromatin/chromosome structureCTF4 MCM16 YPR046W 0 SS Chromatin/chromosome structureCTF4 CLB2 YPR119W 3 SL Cell cycle controlCTF4 CLB5 YPR120C 0 SS Cell cycle controlCTF8 MRC1 YCL060C 0 SL DNA repairCTF8 MRC1 YCL061C 1 SL DNA repairCTF8 RAD57 YDR004W 0 SS DNA repairCTF8 RAD55 YDR076W 0 SS DNA repairCTF8 RAD9 YDR217C 0 SS DNA repairCTF8 HTA1 YDR225W 3 SS Chromatin/chromosome structureCTF8 MSN5 YDR335W 1 SS Nuclear-cytoplasmic transportCTF8 GIM4 YEL003W 2 SS Cell structure

Page 67: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

CTF8 CIN8 YEL061C 0 SL MitosisCTF8 BIM1 YER016W 2 SL MitosisCTF8 SLX8 YER116C 0 SL DNA repairCTF8 CDC26 YFR036W 1 SL Cell cycle controlCTF8 SSF73 YGL066W 3 SS Pol II transcriptionCTF8 MAD1 YGL086W 2 SS MitosisCTF8 SOH1 YGL127C 0 SS DNA repairCTF8 RAD54 YGL163C 0 SS DNA repairCTF8 PMR1 YGL167C 2 SS Small molecule transportCTF8 HUR1 YGL168W 2 SS UnknownCTF8 KEM1 YGL173C 3 SS RNA processingCTF8 KIP3 YGL216W 0 SS MitosisCTF8 RTF1 YGL244W 2 SS Pol II transcriptionCTF8 PAC10 YGR078C 3 SS Cell structureCTF8 UBR1 YGR184C 0 SS Protein degradationCTF8 SMI1 YGR229C 2 SS Cell wall organization and biogenesisCTF8 RRM3 YHR031C 0 SS DNA replicationCTF8 MAD2 YJL030W 3 SS MitosisCTF8 HPR5 YJL092W 0 SS DNA repairCTF8 RAD5 YLR032W 1 SS DNA repairCTF8 ARP6 YLR085C 1 SS Cell structureCTF8 TOP3 YLR234W 0 SS Chromatin/chromosome structureCTF8 YLR235C YLR235C 0 SS UnknownCTF8 RAD52 YML032C 0 SS DNA repairCTF8 GIM5 YML094W 0 SS Cell structureCTF8 LYS7 YMR038C 0 SS Amino-acid metabolismCTF8 CSM3 YMR048W 2 SL MeiosisCTF8 BUB2 YMR055C 0 SS MitosisCTF8 GIM3 YNL153C 2 SS Cell structureCTF8 RAD50 YNL250W 0 SS DNA repairCTF8 TOF1 YNL273W 2 SL DNA repairCTF8 CLA4 YNL298W 3 SS Cell polarityCTF8 HTZ1 YOL012C 0 SS Chromatin/chromosome structureCTF8 ASE1 YOR058C 0 SS MitosisCTF8 SLK19 YOR195W 2 SS Chromatin/chromosome structureCTF8 RAD17 YOR368W 1 SS DNA repairCTF8 CHL1 YPL008W 3 SL Chromatin/chromosome structureCTF8 LGE1 YPL055C 0 SS Cell cycle controlCTF8 DDC1 YPL194W 0 SS DNA repairCTF8 VIK1 YPL253C 2 SS MitosisCTF8 YPR045C YPR045C 0 SL UnknownCTF8 CLB2 YPR119W 2 SS Cell cycle controlCTF8 CTF4 YPR135W 2 SL Chromatin/chromosome structureCTF8 KAR3 YPR141C 3 SL MitosisCTF18 LTE1 YAL024C 0 SL Cell cycle controlCTF18 NUP60 YAR002W 0 SL Nuclear-cytoplasmic transportCTF18 MUM2 YBR057C 0 SL MeiosisCTF18 UBC4 YBR082C 1 SL Protein degradationCTF18 MRPL36 YBR122C 0 SL Protein synthesisCTF18 MRC1 YCL060C 3 SL DNA repairCTF18 MRC1 YCL061C 1 SL DNA repairCTF18 RAD57 YDR004W 0 SS DNA repairCTF18 RAD55 YDR076W 1 SS DNA repairCTF18 RAD9 YDR217C 0 SL DNA repairCTF18 GIM4 YEL003W 0 SL Cell structureCTF18 RAD23 YEL037C 1 SS DNA repairCTF18 CIN8 YEL061C 0 SL MitosisCTF18 PAC2 YER007W 0 SL Cell structureCTF18 BIM1 YER016W 2 SL MitosisCTF18 RAD51 YER095W 1 SS DNA repairCTF18 SLX8 YER116C 1 SL DNA repair

Page 68: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

CTF18 RAD24 YER173W 0 SL DNA repairCTF18 CDC26 YFR036W 2 SL Cell cycle controlCTF18 MAD1 YGL086W 2 SL MitosisCTF18 SOH1 YGL127C 1 SS DNA repairCTF18 RAD54 YGL163C 0 SS DNA repairCTF18 KIP3 YGL216W 0 SL MitosisCTF18 YGL217C YGL217C 1 SS UnknownCTF18 PAC10 YGR078C 0 SL Cell structureCTF18 BUB1 YGR188C 0 SL MitosisCTF18 MAD3 YJL013C 0 SL MitosisCTF18 MAD2 YJL030W 0 SS MitosisCTF18 HPR5 YJL092W 2 SL DNA repairCTF18 POL32 YJR043C 0 SL DNA replicationCTF18 RPS4A YJR145C 3 SL Protein synthesisCTF18 ELM1 YKL048C 0 SL Cell polarityCTF18 HSL1 YKL101W 0 SL Cell cycle controlCTF18 RAD27 YKL113C 1 SS DNA repairCTF18 RAD5 YLR032W 0 SS DNA repairCTF18 ARP6 YLR085C 1 SS Cell structureCTF18 CLB4 YLR210W 1 SS Cell cycle controlCTF18 TOP3 YLR234W 1 SL Chromatin/chromosome structureCTF18 VPS63 YLR261C 1 SS Vacuolar organization and biogenesisCTF18 RAD52 YML032C 1 SS DNA repairCTF18 GIM5 YML094W 0 SL Cell structureCTF18 LYS7 YMR038C 0 SL Amino-acid metabolismCTF18 CSM3 YMR048W 0 SL MeiosisCTF18 SGS1 YMR190C 1 SL DNA repairCTF18 CIK1 YMR198W 0 SL MitosisCTF18 MRE11 YMR224C 0 SL DNA repairCTF18 GIM3 YNL153C 0 SL Cell structureCTF18 RAD50 YNL250W 0 SL DNA repairCTF18 TOF1 YNL273W 0 SL DNA repairCTF18 CLA4 YNL298W 0 SL Cell polarityCTF18 MCK1 YNL307C 0 SL MeiosisCTF18 HTZ1 YOL012C 0 SL Chromatin/chromosome structureCTF18 BUB3 YOR026W 0 SL MitosisCTF18 SLK19 YOR195W 0 SL Chromatin/chromosome structureCTF18 CIN1 YOR349W 0 SL Cell structureCTF18 CHL1 YPL008W 2 SL Chromatin/chromosome structureCTF18 DDC1 YPL194W 0 SL DNA repairCTF18 YPL205C YPL205C 0 SL MeiosisCTF18 CIN2 YPL241C 0 SL Cell structureCTF18 VIK1 YPL253C 3 SL MitosisCTF18 CLB2 YPR119W 3 SL Cell cycle controlCTF18 CTF4 YPR135W 0 SL Chromatin/chromosome structureDCC1 LTE1 YAL024C 0 SL Cell cycle controlDCC1 NUP60 YAR002W 0 SS Nuclear-cytoplasmic transportDCC1 AOR1 YBR231C 1 SS UnknownDCC1 MRC1 YCL060C 0 SL DNA repairDCC1 MRC1 YCL061C 2 SL DNA repairDCC1 HEX3 YDL013W 1 SS MeiosisDCC1 RPN4 YDL020C 0 SL Protein degradationDCC1 RAD57 YDR004W 1 SS DNA repairDCC1 UME6 YDR207C 1 SL MeiosisDCC1 RAD9 YDR217C 2 SL DNA repairDCC1 RAD23 YEL037C 0 SL DNA repairDCC1 PAC2 YER007W 1 SL Cell structureDCC1 BIM1 YER016W 2 SS MitosisDCC1 ISC1 YER019W 1 SL Lipid metabolismDCC1 RAD51 YER095W 1 SS DNA repairDCC1 CHD1 YER164W 1 SS Chromatin/chromosome structure

Page 69: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

DCC1 SSF73 YGL066W 2 SS SL Pol II transcriptionDCC1 MAD1 YGL086W 2 SL MitosisDCC1 RAD54 YGL163C 1 SS DNA repairDCC1 KEM1 YGL173C 0 SL RNA processingDCC1 RTF1 YGL244W 0 SL Pol II transcriptionDCC1 UBR1 YGR184C 1 SS Protein degradationDCC1 BUB1 YGR188C 1 SL MitosisDCC1 RRM3 YHR031C 1 SL DNA replicationDCC1 RPN10 YHR200W 0 SL Pol II transcriptionDCC1 MAD3 YJL013C 1 SS MitosisDCC1 MAD2 YJL030W 0 SL MitosisDCC1 HPR5 YJL092W 1 SL DNA repairDCC1 POL32 YJR043C 1 SS DNA replicationDCC1 RPS4A YJR145C 0 SS Protein synthesisDCC1 HSL1 YKL101W 1 SL Cell cycle controlDCC1 RAD27 YKL113C 1 SS DNA repairDCC1 YLR235C YLR235C 1 SS UnknownDCC1 TSA1 YML028W 1 SL Cell stressDCC1 RAD52 YML032C 0 SS DNA repairDCC1 GIM5 YML094W 2 SL Cell structureDCC1 LYS7 YMR038C 0 SS Amino-acid metabolismDCC1 CSM3 YMR048W 3 SL MeiosisDCC1 SPT21 YMR179W 1 SL Pol II transcriptionDCC1 SGS1 YMR190C 1 SS DNA repairDCC1 CIK1 YMR198W 3 SL MitosisDCC1 MRE11 YMR224C 0 SL DNA repairDCC1 GIM3 YNL153C 3 SL Cell structureDCC1 RTT106 YNL206C 1 SS UnknownDCC1 RAD50 YNL250W 1 SL DNA repairDCC1 TOF1 YNL273W 2 SS DNA repairDCC1 CLA4 YNL298W 3 SL Cell polarityDCC1 HTZ1 YOL012C 3 SS Chromatin/chromosome structureDCC1 SLK19 YOR195W 1 SL Chromatin/chromosome structureDCC1 CIN1 YOR349W 2 SS Cell structureDCC1 CHL1 YPL008W 3 SS Chromatin/chromosome structureDCC1 DDC1 YPL194W 1 SS DNA repairDCC1 CIN2 YPL241C 1 SL Cell structureDCC1 VMA13 YPR036W 1 SL Vacuolar organization and biogenesisDCC1 CLB2 YPR119W 3 SS Cell cycle controlDCC1 CLB5 YPR120C 0 SL Cell cycle controlDCC1 CTF4 YPR135W 0 SL Chromatin/chromosome structureDCC1 KAR3 YPR141C 0 SL MitosisSCC1-73 DCC1 YCL016C 2 SL Chromatin/chromosome structureSCC1-73 MRC1 YCL060C 3 SL DNA repairSCC1-73 CHL4 YDR254W 1 SS Chromatin/chromosome structureSCC1-73 MCM21 YDR318W 3 SL Chromatin/chromosome structureSCC1-73 CIN8 YEL061C 1 SL MitosisSCC1-73 BIM1 YER016W 1 SS MitosisSCC1-73 YGL250W YGL250W 1 SS UnknownSCC1-73 BUB1 YGR188C 1 SL MitosisSCC1-73 CTF8 YHR191C 3 SL Chromatin/chromosome structureSCC1-73 MCM22 YJR135C 3 SS Chromatin/chromosome structureSCC1-73 CTF3 YLR381W 3 SS Chromatin/chromosome structureSCC1-73 GIM5 YML094W 2 SS Cell structureSCC1-73 CSM3 YMR048W 3 SL MeiosisSCC1-73 CTF18 YMR078C 1 SL Chromatin/chromosome structureSCC1-73 GIM3 YNL153C 2 SS Cell structureSCC1-73 TOF1 YNL273W 3 SL DNA repairSCC1-73 BUB3 YOR026W 0 SS MitosisSCC1-73 CHL1 YPL008W 3 SL Chromatin/chromosome structureSCC1-73 YPL017C YPL017C 3 SL Unknown

Page 70: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

SCC1-73 CTF19 YPL018W 2 SL Chromatin/chromosome structureSCC1-73 MCM16 YPR046W 1 SS Chromatin/chromosome structureSCC1-73 CTF4 YPR135W 1 SL Chromatin/chromosome structureSCC1-73 KAR3 YPR141C 1 SL MitosisCHL1 DCC1 YCL016C 2 SL SL Chromatin/chromosome structureCHL1 MRC1 YCL060C 3 SL DNA repairCHL1 RAD61 YDR014W 2 SS UnknownCHL1 CHL4 YDR254W 2 SS Chromatin/chromosome structureCHL1 MCM21 YDR318W 1 SL Chromatin/chromosome structureCHL1 CIN8 YEL061C 0 SL MitosisCHL1 BIM1 YER016W 3 SL MitosisCHL1 MAD1 YGL086W 3 SL MitosisCHL1 BUB1 YGR188C 0 SL MitosisCHL1 CTF8 YHR191C 2 SL SL Chromatin/chromosome structureCHL1 MAD3 YJL013C 0 SS MitosisCHL1 MAD2 YJL030W 3 SS MitosisCHL1 HPR5 YJL092W 1 SS DNA repairCHL1 MCM22 YJR135C 0 SS Chromatin/chromosome structureCHL1 RAD27 YKL113C 1 SS DNA repairCHL1 YKE2 YLR200W 1 SS Cell structureCHL1 NKP2 YLR315W 0 SS Chromatin/chromosome structureCHL1 CTF3 YLR381W 2 SS Chromatin/chromosome structureCHL1 GIM5 YML094W 1 SL Cell structureCHL1 CTF18 YMR078C 0 SL Chromatin/chromosome structureCHL1 GIM3 YNL153C 2 SL Cell structureCHL1 RTS1 YOR014W 0 SL Cell stressCHL1 ELG1 YOR144C 3 SL SL DNA repairCHL1 CTF19 YPL018W 0 SL Chromatin/chromosome structureCHL1 MCM16 YPR046W 0 SS Chromatin/chromosome structureCHL1 CLB2 YPR119W 1 SS Cell cycle controlMAD2 IML3 YBR107C 0 SS Chromatin/chromosome structureMAD2 SOY YBR194W 0 SS UnknownMAD2 BIK1 YCL029C 0 SS MitosisMAD2 HCM1 YCR065W 3 SL Pol II transcriptionMAD2 CHL4 YDR254W 1 SS Chromatin/chromosome structureMAD2 MCM21 YDR318W 0 SL Chromatin/chromosome structureMAD2 VID21 YDR359C 1 SL UnknownMAD2 GIM4 YEL003W 2 SS Cell structureMAD2 CIN8 YEL061C 1 SL MitosisMAD2 PAC2 YER007W 0 SS Cell structureMAD2 BIM1 YER016W 3 SL MitosisMAD2 YGL060W YGL060W 2 SL UnknownMAD2 PAC10 YGR078C 0 SS Cell structureMAD2 CTF8 YHR191C 1 SS Chromatin/chromosome structureMAD2 YJL064W YJL064W 0 SS UnknownMAD2 MCM22 YJR135C 0 SS Chromatin/chromosome structureMAD2 YKE2 YLR200W 0 SL Cell structureMAD2 CTF3 YLR381W 1 SS Chromatin/chromosome structureMAD2 GIM5 YML094W 0 SS Cell structureMAD2 YML095C-A YML095C-A 1 SS UnknownMAD2 RAS2 YNL098C 1 SS Signal transductionMAD2 GIM3 YNL153C 2 SL Cell structureMAD2 HTZ1 YOL012C 1 SS Chromatin/chromosome structureMAD2 SLK19 YOR195W 1 SS Chromatin/chromosome structureMAD2 CIN1 YOR349W 2 SL Cell structureMAD2 CHL1 YPL008W 0 SS Chromatin/chromosome structureMAD2 YPL017C YPL017C 0 SL UnknownMAD2 CTF19 YPL018W 2 SL Chromatin/chromosome structureMAD2 CIN2 YPL241C 1 SL Cell structureMAD2 MCM16 YPR046W 1 SS Chromatin/chromosome structureMAD2 CTF4 YPR135W 0 SS Chromatin/chromosome structure

Page 71: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

MAD2 KAR3 YPR141C 0 SL MitosisYKE2 VPS8 YAL002W 1 SS Vesicular transportYKE2 SSA1 YAL005C 2 SS Protein foldingYKE2 SWC1 YAL011W 3 SL UnknownYKE2 YAL042C-a YAL043C-a 1 SS UnknownYKE2 SLA1 YBL007C 2 SL Cell polarityYKE2 HAP3 YBL021C 1 SS Pol II transcriptionYKE2 NCL1 YBL024W 1 SL RNA processingYKE2 PIN4 YBL051C 2 SL RNA processingYKE2 SIF2 YBR103W 0 SL Chromatin/chromosome structureYKE2 IML3 YBR107C 0 SL Chromatin/chromosome structureYKE2 RAD16 YBR114W 1 SS DNA repairYKE2 CBP6 YBR120C 2 SS Protein synthesisYKE2 SEC66 YBR171W 2 SL Vesicular transportYKE2 PCH2 YBR186W 1 SS MeiosisYKE2 BEM1 YBR200W 1 SL Cell polarityYKE2 AOR1 YBR231C 3 SL UnknownYKE2 YBR255W YBR255W 1 SS UnknownYKE2 DCC1 YCL016C 3 SL Chromatin/chromosome structureYKE2 BIK1 YCL029C 3 SL MitosisYKE2 SNT1 YCR033W 0 SS Chromatin/chromosome structureYKE2 CSM1 YCR086W 1 SS MeiosisYKE2 RPN4 YDL020C 1 SL Protein degradationYKE2 YDL033C YDL033C 2 SS SS UnknownYKE2 CLB3 YDL155W 1 SS Cell cycle controlYKE2 MKC7 YDR144C 1 SS UnknownYKE2 YDR149C YDR149C 2 SL UnknownYKE2 NUM1 YDR150W 2 SL MitosisYKE2 CPR1 YDR155C 1 SS Protein foldingYKE2 PLP1 YDR183W 1 SS Mating responseYKE2 CHL4 YDR254W 2 SL Chromatin/chromosome structureYKE2 PMP3 YDR276C 1 SL Small molecule transportYKE2 RTT103 YDR289C 1 SS UnknownYKE2 SSD1 YDR293C 2 SS Cell cycle controlYKE2 SUM1 YDR310C 3 SL Chromatin/chromosome structureYKE2 MCM21 YDR318W 0 SS Chromatin/chromosome structureYKE2 SWR1 YDR334W 2 SL UnknownYKE2 YDR360W YDR360W 1 SS UnknownYKE2 DYN2 YDR424C 0 SS MitosisYKE2 VPS72 YDR485C 1 SL Vesicular transportYKE2 PAC11 YDR488C 1 SL MitosisYKE2 SPF1 YEL031W 1 SS Small molecule transportYKE2 YEL041W YEL041W 1 SS UnknownYKE2 MAK10 YEL053C 1 SS Protein modificationYKE2 HAT2 YEL056W 1 SS Chromatin/chromosome structureYKE2 CIN8 YEL061C 1 SS MitosisYKE2 PAC2 YER007W 2 SL Cell structureYKE2 BIM1 YER016W 3 SL MitosisYKE2 ISC1 YER019W 1 SS Lipid metabolismYKE2 BEM2 YER155C 0 SS Cell polarityYKE2 FAB1 YFR019W 0 SL Lipid metabolismYKE2 MAD1 YGL086W 3 SL MitosisYKE2 MMS2 YGL087C 0 SS DNA repairYKE2 KEM1 YGL173C 1 SS RNA processingYKE2 HOS2 YGL194C 1 SS Chromatin/chromosome structureYKE2 HAP2 YGL237C 2 SS Pol II transcriptionYKE2 YGL242C YGL242C 1 SS UnknownYKE2 HXK2 YGL253W 1 SS Carbohydrate metabolismYKE2 UGA1 YGR019W 1 SS Amino-acid metabolismYKE2 SHY1 YGR112W 2 SS Energy generationYKE2 BUB1 YGR188C 0 SL Mitosis

Page 72: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

YKE2 YTA7 YGR270W 1 SS Vacuolar organization and biogenesisYKE2 VPS29 YHR012W 1 SS Vesicular transportYKE2 SLT2 YHR030C 0 SS Cell wall organization and biogenesisYKE2 UBA4 YHR111W 0 SS Protein modificationYKE2 ARP1 YHR129C 2 SS MitosisYKE2 WSS1 YHR134W 1 SS DNA repairYKE2 STB5 YHR178W 0 SS Pol II transcriptionYKE2 CTF8 YHR191C 2 SS Chromatin/chromosome structureYKE2 URM1 YIL008W 1 SS Protein modificationYKE2 CAP2 YIL034C 2 SS Cell structureYKE2 SDS3 YIL084C 1 SS Chromatin/chromosome structureYKE2 PRK1 YIL095W 1 SS Cell polarityYKE2 MAD3 YJL013C 0 SS MitosisYKE2 BBC1 YJL020C 1 SL Cell polarityYKE2 MAD2 YJL030W 3 SL MitosisYKE2 BCK1 YJL095W 1 SS Cell wall organization and biogenesisYKE2 MNN11 YJL183W 2 SS Protein modificationYKE2 RPS22A YJL190C 1 SS Protein synthesisYKE2 CPR7 YJR032W 1 SS Protein foldingYKE2 BFA1 YJR053W 1 SL MitosisYKE2 HOC1 YJR075W 0 SS Cell wall organization and biogenesisYKE2 STE24 YJR117W 3 SL Protein modificationYKE2 MCM22 YJR135C 0 SS Chromatin/chromosome structureYKE2 PAN3 YKL025C 2 SS DNA repairYKE2 ELM1 YKL048C 2 SS Cell polarityYKE2 YKL118W YKL118W 1 SS UnknownYKE2 DYN1 YKR054C 0 SS MitosisYKE2 YLL049W YLL049W 1 SS UnknownYKE2 ARP6 YLR085C 2 SS Cell structureYKE2 YLR089C YLR089C 1 SS Mitochondrion organization and biogenesisYKE2 EST1 YLR233C 0 SS Chromatin/chromosome structureYKE2 TOP3 YLR234W 1 SS Chromatin/chromosome structureYKE2 SEC72 YLR292C 1 SS Protein translocationYKE2 VRP1 YLR337C 1 SS Cell polarityYKE2 CTF3 YLR381W 1 SS Chromatin/chromosome structureYKE2 VAC14 YLR386W 2 SS Vacuolar organization and biogenesisYKE2 PPZ1 YML016C 1 SS Signal transductionYKE2 RAD52 YML032C 1 SS DNA repairYKE2 VPS71 YML041C 2 SS Vesicular transportYKE2 TUB3 YML124C 3 SL Cell structureYKE2 MAC1 YMR021C 0 SS Pol II transcriptionYKE2 BUB2 YMR055C 2 SL MitosisYKE2 CTF18 YMR078C 1 SS Chromatin/chromosome structureYKE2 MYO5 YMR109W 1 SS Cell polarityYKE2 CIN4 YMR138W 3 SL Cell structureYKE2 RIM13 YMR154C 1 SS MeiosisYKE2 RSN1 YMR266W 1 SS UnknownYKE2 JNM1 YMR294W 3 SS MitosisYKE2 YMR299C YMR299C 2 SS MitosisYKE2 ELP6 YMR312W 1 SL Pol II transcriptionYKE2 PET8 YNL003C 2 SS Small molecule transportYKE2 YNL140C YNL140C 1 SS UnknownYKE2 CAF40 YNL288W 1 SS Pol II transcriptionYKE2 RIM21 YNL294C 1 SS UnknownYKE2 CLA4 YNL298W 2 SS Cell polarityYKE2 HTZ1 YOL012C 2 SL Chromatin/chromosome structureYKE2 AHC1 YOR023C 1 SL Protein modificationYKE2 BUB3 YOR026W 0 SL MitosisYKE2 ASE1 YOR058C 0 SS MitosisYKE2 RGA1 YOR127W 1 SS Cell polarityYKE2 RUD3 YOR216C 1 SS Vesicular transport

Page 73: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

YKE2 DSE3 YOR264W 2 SL DifferentiationYKE2 RBL2 YOR265W 3 SL Cell structureYKE2 PNT1 YOR266W 3 SL Mitochondrion organization and biogenesisYKE2 PAC1 YOR269W 2 SS MitosisYKE2 YOR296W YOR296W 1 SS UnknownYKE2 CIN1 YOR349W 3 SL Cell structureYKE2 MNE1 YOR350C 2 SS UnknownYKE2 HAP5 YOR358W 3 SS Pol II transcriptionYKE2 CHL1 YPL008W 2 SL Chromatin/chromosome structureYKE2 YPL017C YPL017C 1 SS UnknownYKE2 CTF19 YPL018W 3 SL Chromatin/chromosome structureYKE2 KIP2 YPL155C 3 SL MitosisYKE2 SET6 YPL165C 0 SS UnknownYKE2 NIP100 YPL174C 2 SL MitosisYKE2 CBP3 YPL215W 2 SS Energy generationYKE2 CIN2 YPL241C 3 SL Cell structureYKE2 VIK1 YPL253C 0 SS MitosisYKE2 KAR9 YPL269W 2 SS MitosisYKE2 EAF3 YPR023C 1 SS Pol II TranscriptionYKE2 MCM16 YPR046W 1 SL Chromatin/chromosome structureYKE2 MED1 YPR070W 0 SS Chromatin/chromosome structureYKE2 CTF4 YPR135W 2 SS Chromatin/chromosome structureYKE2 KAR3 YPR141C 3 SL MitosisPAC10 VPS8 YAL002W 1 SS Vesicular transportPAC10 SWC1 YAL011W 3 SL UnknownPAC10 DRS2 YAL026C 1 SS Vesicular transportPAC10 BUD14 YAR014C 1 SS Cell polarityPAC10 SLA1 YBL007C 1 SL Cell polarityPAC10 NCL1 YBL024W 3 SL RNA processingPAC10 PIN4 YBL051C 1 SS RNA processingPAC10 SIF2 YBR103W 1 SS Chromatin/chromosome structurePAC10 IML3 YBR107C 2 SL Chromatin/chromosome structurePAC10 YBR108W YBR108W 1 SS UnknownPAC10 RAD16 YBR114W 0 SL DNA repairPAC10 SEC66 YBR171W 0 SL Vesicular transportPAC10 AOR1 YBR231C 2 SL UnknownPAC10 YBR255W YBR255W 1 SS UnknownPAC10 DCC1 YCL016C 0 SL Chromatin/chromosome structurePAC10 BIK1 YCL029C 3 SL MitosisPAC10 SNT1 YCR033W 0 SL Chromatin/chromosome structurePAC10 PER1 YCR044C 0 SL Other metabolismPAC10 YCR082W YCR082W 1 SS UnknownPAC10 CSM1 YCR086W 0 SL MeiosisPAC10 RPN4 YDL020C 1 SL Protein degradationPAC10 CLB3 YDL155W 0 SL Cell cycle controlPAC10 UGA3 YDL170W 2 SS Pol II transcriptionPAC10 MKC7 YDR144C 1 SL UnknownPAC10 YDR149C YDR149C 0 SL UnknownPAC10 NUM1 YDR150W 0 SL MitosisPAC10 PLP1 YDR183W 1 SS Mating responsePAC10 CHL4 YDR254W 3 SL Chromatin/chromosome structurePAC10 PMP3 YDR276C 1 SL Small molecule transportPAC10 RTT103 YDR289C 1 SS UnknownPAC10 SSD1 YDR293C 3 SS Cell cycle controlPAC10 SUM1 YDR310C 3 SL Chromatin/chromosome structurePAC10 MCM21 YDR318W 0 SL Chromatin/chromosome structurePAC10 SWR1 YDR334W 1 SL UnknownPAC10 YDR360W YDR360W 1 SS UnknownPAC10 DYN2 YDR424C 0 SL MitosisPAC10 VPS72 YDR485C 1 SS Vesicular transportPAC10 PAC11 YDR488C 0 SL Mitosis

Page 74: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

PAC10 SPF1 YEL031W 2 SS Small molecule transportPAC10 UTR4 YEL038W 1 SS UnknownPAC10 CYC7 YEL039C 1 SL Energy generationPAC10 YEL041W YEL041W 1 SS UnknownPAC10 AFG1 YEL052W 1 SS Protein foldingPAC10 MAK10 YEL053C 2 SL Protein modificationPAC10 HAT2 YEL056W 1 SS Chromatin/chromosome structurePAC10 CIN8 YEL061C 0 SL MitosisPAC10 PAC2 YER007W 3 SL Cell structurePAC10 BIM1 YER016W 3 SL MitosisPAC10 PEA2 YER149C 1 SL Cell polarityPAC10 BEM2 YER155C 1 SS Cell polarityPAC10 BMH1 YER177W 0 SL DifferentiationPAC10 FAB1 YFR019W 0 SL Lipid metabolismPAC10 MAD1 YGL086W 3 SL MitosisPAC10 MMS2 YGL087C 2 SS DNA repairPAC10 KEM1 YGL173C 2 SS RNA processingPAC10 HOS2 YGL194C 1 SS Chromatin/chromosome structurePAC10 YGL242C YGL242C 1 SS UnknownPAC10 HXK2 YGL253W 2 SS Carbohydrate metabolismPAC10 YGR054W YGR054W 2 SS UnknownPAC10 CLB1 YGR108W 2 SS Cell cycle controlPAC10 SHY1 YGR112W 2 SS Energy generationPAC10 SMI1 YGR229C 1 SL Cell wall organization and biogenesisPAC10 HSE1 YHL002W 0 SS TransportPAC10 YHL029C YHL029C 2 SS UnknownPAC10 VPS29 YHR012W 2 SS Vesicular transportPAC10 UBA4 YHR111W 2 SS Protein modificationPAC10 BZZ1 YHR114W 0 SS Cell polarityPAC10 ARP1 YHR129C 0 SS MitosisPAC10 WSS1 YHR134W 1 SS DNA repairPAC10 STB5 YHR178W 2 SS Pol II transcriptionPAC10 CTF8 YHR191C 0 SS Chromatin/chromosome structurePAC10 URM1 YIL008W 1 SS Protein modificationPAC10 CAP2 YIL034C 1 SS Cell structurePAC10 SDS3 YIL084C 1 SS Chromatin/chromosome structurePAC10 PRK1 YIL095W 1 SS Cell polarityPAC10 MAD3 YJL013C 0 SL MitosisPAC10 BBC1 YJL020C 1 SS Cell polarityPAC10 MAD2 YJL030W 0 SL MitosisPAC10 RPS22A YJL190C 1 SS Protein synthesisPAC10 CPR7 YJR032W 0 SL Protein foldingPAC10 BFA1 YJR053W 3 SL MitosisPAC10 HOC1 YJR075W 3 SS Cell wall organization and biogenesisPAC10 STE24 YJR117W 2 SL Protein modificationPAC10 YJR129C YJR129C 2 SL UnknownPAC10 MCM22 YJR135C 2 SL Chromatin/chromosome structurePAC10 ELM1 YKL048C 1 SS Cell polarityPAC10 DYN1 YKR054C 0 SS MitosisPAC10 DNM1 YLL001W 1 SS Cell structurePAC10 MMM1 YLL006W 1 SS Cell structurePAC10 YLL007C YLL007C 1 SS UnknownPAC10 YLL049W YLL049W 2 SL UnknownPAC10 ARP6 YLR085C 1 SL Cell structurePAC10 YLR089C YLR089C 2 SL Mitochondrion organization and biogenesisPAC10 CLB4 YLR210W 0 SS Cell cycle controlPAC10 TOP3 YLR234W 1 SS Chromatin/chromosome structurePAC10 SEC72 YLR292C 3 SL Protein translocationPAC10 VRP1 YLR337C 1 SL Cell polarityPAC10 CTF3 YLR381W 2 SL Chromatin/chromosome structurePAC10 RAD52 YML032C 1 SS DNA repair

Page 75: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

PAC10 TUB3 YML124C 3 SL Cell structurePAC10 BUB2 YMR055C 0 SS MitosisPAC10 CTF18 YMR078C 0 SL Chromatin/chromosome structurePAC10 MYO5 YMR109W 1 SS Cell polarityPAC10 CIN4 YMR138W 2 SS Cell structurePAC10 RIM13 YMR154C 1 SS MeiosisPAC10 HOT1 YMR172W 1 SS Cell stressPAC10 JNM1 YMR294W 3 SL MitosisPAC10 YMR299C YMR299C 1 SS MitosisPAC10 ELP6 YMR312W 2 SS Pol II transcriptionPAC10 YNL140C YNL140C 1 SS UnknownPAC10 BNI5 YNL166C 1 SL CytokinesisPAC10 CAF40 YNL288W 1 SL Pol II transcriptionPAC10 RIM21 YNL294C 1 SL UnknownPAC10 CLA4 YNL298W 0 SS Cell polarityPAC10 HTZ1 YOL012C 0 SL Chromatin/chromosome structurePAC10 RTG1 YOL067C 1 SS Carbohydrate metabolismPAC10 AHC1 YOR023C 0 SL Protein modificationPAC10 BUB3 YOR026W 1 SS MitosisPAC10 ASE1 YOR058C 2 SS MitosisPAC10 RGA1 YOR127W 0 SL Cell polarityPAC10 VPS17 YOR132W 2 SL Vesicular transportPAC10 RUD3 YOR216C 2 SL Vesicular transportPAC10 DSE3 YOR264W 3 SL DifferentiationPAC10 RBL2 YOR265W 3 SL Cell structurePAC10 PNT1 YOR266W 3 SL Mitochondrion organization and biogenesisPAC10 PAC1 YOR269W 3 SL MitosisPAC10 SPS4 YOR313C 0 SS MeiosisPAC10 CIN1 YOR349W 3 SL Cell structurePAC10 CHL1 YPL008W 0 SL Chromatin/chromosome structurePAC10 YPL017C YPL017C 1 SS UnknownPAC10 CTF19 YPL018W 0 SL Chromatin/chromosome structurePAC10 BEM3 YPL115C 1 SL Cell polarityPAC10 KIP2 YPL155C 3 SS MitosisPAC10 BEM4 YPL161C 1 SS Cell polarityPAC10 SET6 YPL165C 2 SS UnknownPAC10 NIP100 YPL174C 3 SL MitosisPAC10 CIN2 YPL241C 3 SL Cell structurePAC10 VIK1 YPL253C 3 SL MitosisPAC10 KAR9 YPL269W 0 SL MitosisPAC10 EAF3 YPR023C 1 SS Pol II TranscriptionPAC10 MCM16 YPR046W 1 SS Chromatin/chromosome structurePAC10 YPR050C YPR050C 2 SL UnknownPAC10 MAK3 YPR051W 1 SS Protein modificationPAC10 MED1 YPR070W 1 SS Chromatin/chromosome structurePAC10 CTF4 YPR135W 1 SL Chromatin/chromosome structurePAC10 KAR3 YPR141C 1 SS MitosisGIM3 SWC1 YAL011W 2 SL UnknownGIM3 SLA1 YBL007C 3 SL Cell polarityGIM3 NCL1 YBL024W 0 SL RNA processingGIM3 SIF2 YBR103W 1 SS Chromatin/chromosome structureGIM3 IML3 YBR107C 1 SS Chromatin/chromosome structureGIM3 YBR108W YBR108W 1 SS UnknownGIM3 SEC66 YBR171W 2 SL Vesicular transportGIM3 BEM1 YBR200W 0 SL Cell polarityGIM3 AOR1 YBR231C 0 SL UnknownGIM3 BSD2 YBR290W 1 SS TransportGIM3 DCC1 YCL016C 3 SL Chromatin/chromosome structureGIM3 BIK1 YCL029C 3 SL MitosisGIM3 PER1 YCR044C 1 SS Other metabolismGIM3 CSM1 YCR086W 1 SS Meiosis

Page 76: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

GIM3 CLB3 YDL155W 1 SS Cell cycle controlGIM3 UGA3 YDL170W 1 SS Pol II transcriptionGIM3 YDR149C YDR149C 3 SS UnknownGIM3 NUM1 YDR150W 3 SS MitosisGIM3 PLP1 YDR183W 2 SS Mating responseGIM3 CHL4 YDR254W 0 SL Chromatin/chromosome structureGIM3 PMP3 YDR276C 1 SS Small molecule transportGIM3 RTT103 YDR289C 0 SS UnknownGIM3 SSD1 YDR293C 0 SS Cell cycle controlGIM3 SUM1 YDR310C 3 SL Chromatin/chromosome structureGIM3 MCM21 YDR318W 2 SL Chromatin/chromosome structureGIM3 SWR1 YDR334W 2 SL UnknownGIM3 YDR360W YDR360W 1 SS UnknownGIM3 DYN2 YDR424C 2 SS MitosisGIM3 VPS72 YDR485C 2 SL Vesicular transportGIM3 PAC11 YDR488C 1 SS MitosisGIM3 CIN8 YEL061C 0 SL MitosisGIM3 PAC2 YER007W 3 SL Cell structureGIM3 BIM1 YER016W 3 SL MitosisGIM3 BEM2 YER155C 2 SL Cell polarityGIM3 BMH1 YER177W 1 SS DifferentiationGIM3 FAB1 YFR019W 2 SL Lipid metabolismGIM3 MAD1 YGL086W 3 SL MitosisGIM3 HXK2 YGL253W 1 SL Carbohydrate metabolismGIM3 YGR054W YGR054W 1 SS UnknownGIM3 BUB1 YGR188C 0 SL MitosisGIM3 SMI1 YGR229C 1 SS Cell wall organization and biogenesisGIM3 YTA7 YGR270W 1 SS Vacuolar organization and biogenesisGIM3 VPS29 YHR012W 2 SS Vesicular transportGIM3 SLT2 YHR030C 1 SS Cell wall organization and biogenesisGIM3 UBA4 YHR111W 0 SS Protein modificationGIM3 ARP1 YHR129C 3 SL MitosisGIM3 STB5 YHR178W 1 SL Pol II transcriptionGIM3 CTF8 YHR191C 0 SL Chromatin/chromosome structureGIM3 PRK1 YIL095W 1 SS Cell polarityGIM3 MAD3 YJL013C 1 SL MitosisGIM3 BBC1 YJL020C 1 SS Cell polarityGIM3 MAD2 YJL030W 2 SL MitosisGIM3 BCK1 YJL095W 0 SL Cell wall organization and biogenesisGIM3 MNN11 YJL183W 1 SS Protein modificationGIM3 RPS22A YJL190C 1 SL Protein synthesisGIM3 CPR7 YJR032W 2 SS Protein foldingGIM3 BFA1 YJR053W 3 SL MitosisGIM3 HOC1 YJR075W 3 SL Cell wall organization and biogenesisGIM3 STE24 YJR117W 3 SL Protein modificationGIM3 MCM22 YJR135C 2 SL Chromatin/chromosome structureGIM3 PAN3 YKL025C 3 SS DNA repairGIM3 ELM1 YKL048C 2 SL Cell polarityGIM3 YKL118W YKL118W 1 SS UnknownGIM3 DYN1 YKR054C 2 SL MitosisGIM3 MMM1 YLL006W 2 SS Cell structureGIM3 YLL049W YLL049W 1 SS UnknownGIM3 ARP6 YLR085C 3 SL Cell structureGIM3 YLR089C YLR089C 2 SL Mitochondrion organization and biogenesisGIM3 VRP1 YLR337C 0 SL Cell polarityGIM3 CTF3 YLR381W 2 SL Chromatin/chromosome structureGIM3 VAC14 YLR386W 3 SS Vacuolar organization and biogenesisGIM3 VMA6 YLR447C 1 SS Vacuolar organization and biogenesisGIM3 RAD52 YML032C 2 SS DNA repairGIM3 VPS71 YML041C 3 SL Vesicular transportGIM3 TUB3 YML124C 3 SL Cell structure

Page 77: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

GIM3 BUB2 YMR055C 3 SL MitosisGIM3 CTF18 YMR078C 0 SS SL Chromatin/chromosome structureGIM3 MYO5 YMR109W 0 SL Cell polarityGIM3 CIN4 YMR138W 3 SL Cell structureGIM3 RIM13 YMR154C 1 SS MeiosisGIM3 JNM1 YMR294W 3 SL MitosisGIM3 YMR299C YMR299C 2 SL MitosisGIM3 ELP6 YMR312W 1 SS Pol II transcriptionGIM3 BNI5 YNL166C 1 SL CytokinesisGIM3 RIM21 YNL294C 1 SS UnknownGIM3 CLA4 YNL298W 0 SL Cell polarityGIM3 HTZ1 YOL012C 0 SL Chromatin/chromosome structureGIM3 AHC1 YOR023C 1 SL Protein modificationGIM3 BUB3 YOR026W 0 SL MitosisGIM3 ASE1 YOR058C 2 SL MitosisGIM3 RUD3 YOR216C 3 SL Vesicular transportGIM3 DSE3 YOR264W 2 SL DifferentiationGIM3 RBL2 YOR265W 3 SL Cell structureGIM3 PNT1 YOR266W 3 SL Mitochondrion organization and biogenesisGIM3 PAC1 YOR269W 2 SL MitosisGIM3 CIN1 YOR349W 3 SL Cell structureGIM3 HAP5 YOR358W 1 SS Pol II transcriptionGIM3 CHL1 YPL008W 0 SL Chromatin/chromosome structureGIM3 YPL017C YPL017C 1 SS UnknownGIM3 CTF19 YPL018W 2 SL Chromatin/chromosome structureGIM3 BEM3 YPL115C 1 SS Cell polarityGIM3 KIP2 YPL155C 2 SL MitosisGIM3 SET6 YPL165C 1 SS UnknownGIM3 NIP100 YPL174C 3 SL MitosisGIM3 CIN2 YPL241C 3 SL Cell structureGIM3 VIK1 YPL253C 0 SL MitosisGIM3 KAR9 YPL269W 2 SL MitosisGIM3 EAF3 YPR023C 1 SS Pol II TranscriptionGIM3 MCM16 YPR046W 1 SS Chromatin/chromosome structureGIM3 MED1 YPR070W 1 SS Chromatin/chromosome structureGIM3 CTF4 YPR135W 1 SL Chromatin/chromosome structureGIM3 KAR3 YPR141C 0 SL MitosisGIM4 SWC1 YAL011W 3 SL UnknownGIM4 SLA1 YBL007C 1 SS Cell polarityGIM4 NCL1 YBL024W 3 SS RNA processingGIM4 PIN4 YBL051C 1 SS RNA processingGIM4 SIF2 YBR103W 2 SS Chromatin/chromosome structureGIM4 IML3 YBR107C 1 SS Chromatin/chromosome structureGIM4 SEC66 YBR171W 0 SS Vesicular transportGIM4 AOR1 YBR231C 2 SS UnknownGIM4 DCC1 YCL016C 3 SL Chromatin/chromosome structureGIM4 BIK1 YCL029C 2 SL MitosisGIM4 PER1 YCR044C 1 SS Other metabolismGIM4 YCR082W YCR082W 2 SS SL UnknownGIM4 CSM1 YCR086W 2 SL MeiosisGIM4 CBS1 YDL069C 1 SS Protein synthesisGIM4 CLB3 YDL155W 2 SS Cell cycle controlGIM4 YDR149C YDR149C 2 SS UnknownGIM4 NUM1 YDR150W 0 SS MitosisGIM4 CPR1 YDR155C 0 SS Protein foldingGIM4 CHL4 YDR254W 0 SS Chromatin/chromosome structureGIM4 PMP3 YDR276C 2 SS Small molecule transportGIM4 RTT103 YDR289C 0 SS UnknownGIM4 MCM21 YDR318W 2 SS Chromatin/chromosome structureGIM4 SWR1 YDR334W 2 SL UnknownGIM4 DYN2 YDR424C 0 SL Mitosis

Page 78: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

GIM4 VPS72 YDR485C 0 SL Vesicular transportGIM4 PAC11 YDR488C 1 SS MitosisGIM4 CIN8 YEL061C 2 SL MitosisGIM4 PAC2 YER007W 1 SL Cell structureGIM4 BIM1 YER016W 3 SL MitosisGIM4 ISC1 YER019W 1 SS Lipid metabolismGIM4 PEA2 YER149C 1 SS Cell polarityGIM4 BEM2 YER155C 1 SS Cell polarityGIM4 BMH1 YER177W 1 SS DifferentiationGIM4 FAB1 YFR019W 0 SL Lipid metabolismGIM4 MAD1 YGL086W 3 SL MitosisGIM4 MMS2 YGL087C 0 SS DNA repairGIM4 HXK2 YGL253W 0 SS Carbohydrate metabolismGIM4 BUB1 YGR188C 0 SL MitosisGIM4 YTA7 YGR270W 0 SL Vacuolar organization and biogenesisGIM4 HSE1 YHL002W 1 SS TransportGIM4 VPS29 YHR012W 1 SL Vesicular transportGIM4 UBA4 YHR111W 1 SS Protein modificationGIM4 ARP1 YHR129C 3 SS MitosisGIM4 CTF8 YHR191C 0 SL Chromatin/chromosome structureGIM4 CAP2 YIL034C 0 SS Cell structureGIM4 SDS3 YIL084C 0 SS Chromatin/chromosome structureGIM4 PRK1 YIL095W 0 SL Cell polarityGIM4 MAD3 YJL013C 2 SS MitosisGIM4 BBC1 YJL020C 0 SL Cell polarityGIM4 MAD2 YJL030W 3 SL MitosisGIM4 MNN11 YJL183W 2 SL Protein modificationGIM4 RPS22A YJL190C 0 SS Protein synthesisGIM4 CPR7 YJR032W 1 SS Protein foldingGIM4 BFA1 YJR053W 2 SL MitosisGIM4 HOC1 YJR075W 0 SS Cell wall organization and biogenesisGIM4 STE24 YJR117W 3 SL Protein modificationGIM4 YJR129C YJR129C 0 SS UnknownGIM4 MCM22 YJR135C 0 SS Chromatin/chromosome structureGIM4 PAN3 YKL025C 2 SL DNA repairGIM4 ELM1 YKL048C 3 SL Cell polarityGIM4 YKL118W YKL118W 3 SL UnknownGIM4 DYN1 YKR054C 0 SS MitosisGIM4 DNM1 YLL001W 1 SS Cell structureGIM4 MMM1 YLL006W 0 SL Cell structureGIM4 YLL007C YLL007C 1 SS UnknownGIM4 YLL049W YLL049W 2 SS UnknownGIM4 ARP6 YLR085C 3 SL Cell structureGIM4 YLR089C YLR089C 1 SL Mitochondrion organization and biogenesisGIM4 SEC72 YLR292C 1 SS Protein translocationGIM4 VRP1 YLR337C 0 SL Cell polarityGIM4 CTF3 YLR381W 0 SS Chromatin/chromosome structureGIM4 VAC14 YLR386W 1 SS Vacuolar organization and biogenesisGIM4 VMA6 YLR447C 0 SL Vacuolar organization and biogenesisGIM4 RAD52 YML032C 1 SS DNA repairGIM4 VPS71 YML041C 3 SL Vesicular transportGIM4 RAD10 YML095C 0 SS DNA repairGIM4 TUB3 YML124C 3 SL Cell structureGIM4 MSC1 YML128C 0 SL UnknownGIM4 BUB2 YMR055C 0 SS MitosisGIM4 CTF18 YMR078C 0 SL Chromatin/chromosome structureGIM4 MYO5 YMR109W 0 SL Cell polarityGIM4 CIN4 YMR138W 3 SL Cell structureGIM4 RIM13 YMR154C 1 SS MeiosisGIM4 JNM1 YMR294W 2 SS MitosisGIM4 YMR299C YMR299C 1 SS Mitosis

Page 79: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

GIM4 ELP6 YMR312W 1 SS Pol II transcriptionGIM4 YNL140C YNL140C 1 SS UnknownGIM4 RIM21 YNL294C 1 SS UnknownGIM4 CLA4 YNL298W 0 SS Cell polarityGIM4 HTZ1 YOL012C 3 SL Chromatin/chromosome structureGIM4 MSN1 YOL116W 0 SS Cell stressGIM4 AHC1 YOR023C 1 SS Protein modificationGIM4 BUB3 YOR026W 1 SS MitosisGIM4 ASE1 YOR058C 0 SS MitosisGIM4 RGA1 YOR127W 1 SS Cell polarityGIM4 RUD3 YOR216C 1 SS Vesicular transportGIM4 DSE3 YOR264W 3 SL DifferentiationGIM4 RBL2 YOR265W 3 SL Cell structureGIM4 PNT1 YOR266W 3 SL Mitochondrion organization and biogenesisGIM4 PAC1 YOR269W 0 SL MitosisGIM4 CIN1 YOR349W 3 SL Cell structureGIM4 HAP5 YOR358W 1 SS Pol II transcriptionGIM4 CHL1 YPL008W 0 SL Chromatin/chromosome structureGIM4 YPL017C YPL017C 1 SS UnknownGIM4 CTF19 YPL018W 2 SL Chromatin/chromosome structureGIM4 KIP2 YPL155C 0 SL MitosisGIM4 BEM4 YPL161C 0 SS Cell polarityGIM4 NIP100 YPL174C 0 SS MitosisGIM4 MMT2 YPL224C 1 SS Small molecule transportGIM4 CIN2 YPL241C 3 SL Cell structureGIM4 VIK1 YPL253C 0 SS MitosisGIM4 KAR9 YPL269W 0 SL MitosisGIM4 EAF3 YPR023C 0 SS Pol II TranscriptionGIM4 MCM16 YPR046W 0 SS SS Chromatin/chromosome structureGIM4 YPR050C YPR050C 1 SS UnknownGIM4 MED1 YPR070W 1 SL Chromatin/chromosome structureGIM4 CTF4 YPR135W 1 SL Chromatin/chromosome structureGIM4 KAR3 YPR141C 0 SL MitosisGIM5 VPS8 YAL002W 0 SS SS Vesicular transportGIM5 SWC1 YAL011W 1 SS UnknownGIM5 DRS2 YAL026C 1 SL Vesicular transportGIM5 SLA1 YBL007C 0 SS SL Cell polarityGIM5 NCL1 YBL024W 0 SS RNA processingGIM5 PIN4 YBL051C 1 SS RNA processingGIM5 SIF2 YBR103W 1 SS Chromatin/chromosome structureGIM5 IML3 YBR107C 1 SS Chromatin/chromosome structureGIM5 YBR108W YBR108W 1 SS UnknownGIM5 SEC66 YBR171W 2 SL Vesicular transportGIM5 AOR1 YBR231C 1 SS UnknownGIM5 YBR255W YBR255W 1 SS UnknownGIM5 BSD2 YBR290W 1 SS TransportGIM5 DCC1 YCL016C 2 SL Chromatin/chromosome structureGIM5 BIK1 YCL029C 3 SL MitosisGIM5 CSM1 YCR086W 1 SS MeiosisGIM5 RPN4 YDL020C 1 SS Protein degradationGIM5 CLB3 YDL155W 2 SS Cell cycle controlGIM5 MKC7 YDR144C 1 SS UnknownGIM5 YDR149C YDR149C 1 SS UnknownGIM5 NUM1 YDR150W 1 SL MitosisGIM5 PLP1 YDR183W 1 SS Mating responseGIM5 CHL4 YDR254W 1 SS Chromatin/chromosome structureGIM5 PMP3 YDR276C 1 SL Small molecule transportGIM5 SSD1 YDR293C 2 SS Cell cycle controlGIM5 SUM1 YDR310C 1 SL Chromatin/chromosome structureGIM5 MCM21 YDR318W 2 SS Chromatin/chromosome structureGIM5 SWR1 YDR334W 0 SL Unknown

Page 80: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

GIM5 YDR360W YDR360W 1 SS UnknownGIM5 DYN2 YDR424C 2 SS MitosisGIM5 VPS72 YDR485C 0 SL Vesicular transportGIM5 PAC11 YDR488C 1 SS MitosisGIM5 SPF1 YEL031W 0 SS Small molecule transportGIM5 MAK10 YEL053C 3 SS Protein modificationGIM5 CIN8 YEL061C 1 SL MitosisGIM5 PAC2 YER007W 3 SL Cell structureGIM5 BIM1 YER016W 0 SL MitosisGIM5 KAP123 YER110C 1 SS Nuclear-cytoplasmic transportGIM5 BEM2 YER155C 1 SS Cell polarityGIM5 BMH1 YER177W 1 SS DifferentiationGIM5 FAB1 YFR019W 2 SS Lipid metabolismGIM5 MAD1 YGL086W 3 SS MitosisGIM5 MMS2 YGL087C 3 SS DNA repairGIM5 MON1 YGL124C 1 SS UnknownGIM5 NUT1 YGL151W 1 SS Pol II transcriptionGIM5 KEM1 YGL173C 1 SL RNA processingGIM5 HOS2 YGL194C 1 SS Chromatin/chromosome structureGIM5 HXK2 YGL253W 1 SS Carbohydrate metabolismGIM5 UGA1 YGR019W 1 SS Amino-acid metabolismGIM5 YGR054W YGR054W 1 SS UnknownGIM5 BUB1 YGR188C 1 SL MitosisGIM5 SMI1 YGR229C 1 SS Cell wall organization and biogenesisGIM5 YTA7 YGR270W 1 SS Vacuolar organization and biogenesisGIM5 YHL029C YHL029C 1 SS UnknownGIM5 VPS29 YHR012W 1 SS Vesicular transportGIM5 SLT2 YHR030C 1 SS Cell wall organization and biogenesisGIM5 UBA4 YHR111W 1 SS Protein modificationGIM5 BZZ1 YHR114W 1 SS Cell polarityGIM5 ARP1 YHR129C 1 SS MitosisGIM5 WSS1 YHR134W 1 SS DNA repairGIM5 STB5 YHR178W 1 SS Pol II transcriptionGIM5 CTF8 YHR191C 0 SS Chromatin/chromosome structureGIM5 URM1 YIL008W 1 SS Protein modificationGIM5 CAP2 YIL034C 1 SS Cell structureGIM5 PRK1 YIL095W 0 SS Cell polarityGIM5 MAD3 YJL013C 1 SS MitosisGIM5 BBC1 YJL020C 1 SS Cell polarityGIM5 MAD2 YJL030W 3 SS MitosisGIM5 BCK1 YJL095W 0 SS Cell wall organization and biogenesisGIM5 VPS35 YJL154C 1 SS Vesicular transportGIM5 RPS22A YJL190C 1 SS Protein synthesisGIM5 CPR7 YJR032W 1 SS Protein foldingGIM5 BFA1 YJR053W 2 SS MitosisGIM5 HOC1 YJR075W 3 SS Cell wall organization and biogenesisGIM5 STE24 YJR117W 2 SS Protein modificationGIM5 MCM22 YJR135C 0 SL Chromatin/chromosome structureGIM5 PAN3 YKL025C 3 SS DNA repairGIM5 ELM1 YKL048C 1 SS Cell polarityGIM5 YKL118W YKL118W 1 SS UnknownGIM5 DYN1 YKR054C 0 SS MitosisGIM5 DNM1 YLL001W 1 SS Cell structureGIM5 MMM1 YLL006W 1 SS Cell structureGIM5 YLL007C YLL007C 1 SS UnknownGIM5 YLL049W YLL049W 1 SL UnknownGIM5 ARP6 YLR085C 1 SL Cell structureGIM5 YLR089C YLR089C 1 SL Mitochondrion organization and biogenesisGIM5 SEC72 YLR292C 1 SS Protein translocationGIM5 VRP1 YLR337C 1 SL Cell polarityGIM5 VPS38 YLR360W 1 SS SL Vesicular transport

Page 81: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

GIM5 CTF3 YLR381W 1 SS Chromatin/chromosome structureGIM5 VAC14 YLR386W 3 SL Vacuolar organization and biogenesisGIM5 VMA6 YLR447C 1 SS Vacuolar organization and biogenesisGIM5 RAD52 YML032C 1 SS DNA repairGIM5 VPS71 YML041C 2 SS Vesicular transportGIM5 GSF2 YML048W 1 SS Carbohydrate metabolismGIM5 TUB3 YML124C 2 SS Cell structureGIM5 MSC1 YML128C 1 SS UnknownGIM5 MAC1 YMR021C 1 SS Pol II transcriptionGIM5 BUB2 YMR055C 0 SS MitosisGIM5 CTF18 YMR078C 0 SL Chromatin/chromosome structureGIM5 MYO5 YMR109W 1 SL Cell polarityGIM5 SAS2 YMR127C 0 SS Chromatin/chromosome structureGIM5 CIN4 YMR138W 2 SS Cell structureGIM5 RIM13 YMR154C 1 SS MeiosisGIM5 HOT1 YMR172W 1 SL Cell stressGIM5 RSN1 YMR266W 1 SS UnknownGIM5 JNM1 YMR294W 0 SS MitosisGIM5 YMR299C YMR299C 1 SS MitosisGIM5 ELP6 YMR312W 1 SS Pol II transcriptionGIM5 YNL140C YNL140C 1 SS UnknownGIM5 BNI5 YNL166C 0 SS SS CytokinesisGIM5 CAF40 YNL288W 1 SS Pol II transcriptionGIM5 RIM21 YNL294C 1 SL UnknownGIM5 CLA4 YNL298W 1 SS Cell polarityGIM5 HTZ1 YOL012C 1 SL Chromatin/chromosome structureGIM5 RTG1 YOL067C 1 SS Carbohydrate metabolismGIM5 MSN1 YOL116W 1 SS Cell stressGIM5 AHC1 YOR023C 0 SS Protein modificationGIM5 BUB3 YOR026W 1 SL MitosisGIM5 ASE1 YOR058C 2 SS MitosisGIM5 VPS17 YOR132W 3 SS Vesicular transportGIM5 RUD3 YOR216C 3 SS Vesicular transportGIM5 DSE3 YOR264W 2 SS DifferentiationGIM5 RBL2 YOR265W 3 SS Cell structureGIM5 PNT1 YOR266W 3 SS Mitochondrion organization and biogenesisGIM5 PAC1 YOR269W 0 SS MitosisGIM5 CIN1 YOR349W 3 SS Cell structureGIM5 CHL1 YPL008W 1 SS Chromatin/chromosome structureGIM5 YPL017C YPL017C 0 SL UnknownGIM5 CTF19 YPL018W 1 SS Chromatin/chromosome structureGIM5 BEM3 YPL115C 1 SS Cell polarityGIM5 KIP2 YPL155C 2 SS MitosisGIM5 NIP100 YPL174C 0 SS MitosisGIM5 YPL176C YPL176C 1 SS Cell growth and/or maintenanceGIM5 CIN2 YPL241C 3 SL Cell structureGIM5 VIK1 YPL253C 2 SS MitosisGIM5 KAR9 YPL269W 0 SS MitosisGIM5 EAF3 YPR023C 1 SS Pol II TranscriptionGIM5 MCM16 YPR046W 0 SS Chromatin/chromosome structureGIM5 YPR050C YPR050C 0 SS UnknownGIM5 MAK3 YPR051W 0 SS Protein modificationGIM5 MED1 YPR070W 1 SS Chromatin/chromosome structureGIM5 CTF4 YPR135W 1 SS Chromatin/chromosome structureGIM5 KAR3 YPR141C 0 SL SL MitosisCSM3 DCC1 YCL016C 2 SL SL Chromatin/chromosome structureCSM3 MRC1 YCL060C 3 SS DNA repairCSM3 RAD57 YDR004W 0 SS DNA repairCSM3 RAD9 YDR217C 1 SS DNA repairCSM3 GIM4 YEL003W 0 SS Cell structureCSM3 BIM1 YER016W 3 SL Mitosis

Page 82: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

CSM3 ISC1 YER019W 1 SS Lipid metabolismCSM3 SLX8 YER116C 2 SS SS DNA repairCSM3 RAD4 YER162C 1 SS DNA repairCSM3 RAD24 YER173W 0 SS SS DNA repairCSM3 CDH1 YGL003C 2 SS Protein degradationCSM3 MAD1 YGL086W 0 SS MitosisCSM3 PAC10 YGR078C 0 SS Cell structureCSM3 BUB1 YGR188C 0 SL MitosisCSM3 CTF8 YHR191C 0 SL SL Chromatin/chromosome structureCSM3 APQ12 YIL040W 0 SS UnknownCSM3 HPR5 YJL092W 2 SL DNA repairCSM3 POL32 YJR043C 3 SL SL DNA replicationCSM3 CSN12 YJR084W 0 SL UnknownCSM3 RAD27 YKL113C 0 SS SS DNA repairCSM3 RAD5 YLR032W 1 SS DNA repairCSM3 YKE2 YLR200W 0 SL Cell structureCSM3 TOP3 YLR234W 0 SS Chromatin/chromosome structureCSM3 MEC3 YLR288C 0 SS DNA repairCSM3 SEL1 YML013W 0 SS UnknownCSM3 GIM5 YML094W 0 SS Cell structureCSM3 YMR010W YMR010W 0 SS MeiosisCSM3 BUB2 YMR055C 0 SL MitosisCSM3 CTF18 YMR078C 0 SS SL Chromatin/chromosome structureCSM3 SGS1 YMR190C 1 SS SS DNA repairCSM3 GIM3 YNL153C 0 SS Cell structureCSM3 MON2 YNL297C 0 SS Vacuolar organization and biogenesisCSM3 BRE5 YNR051C 0 SS UnknownCSM3 ELG1 YOR144C 1 SS SS DNA repairCSM3 RAD17 YOR368W 3 SS SS DNA repairCSM3 YPL077C YPL077C 0 SS UnknownCSM3 GUP2 YPL189W 2 SS Lipid metabolismCSM3 DDC1 YPL194W 0 SS DNA repairCSM3 CTF4 YPR135W 0 SL SL Chromatin/chromosome structureCSM3 KAR3 YPR141C 0 SL MitosisMRC1 NUP60 YAR002W 3 SS SS Nuclear-cytoplasmic transportMRC1 PHO5 YBR093C 2 SS SS Phosphate metabolismMRC1 DCC1 YCL016C 1 SL Chromatin/chromosome structureMRC1 RAD9 YDR217C 3 SL SL DNA repairMRC1 XRS2 YDR369C 0 SS SS DNA repairMRC1 RAD51 YER095W 1 SS DNA repairMRC1 RAD24 YER173W 2 SL SS DNA repairMRC1 SOH1 YGL127C 1 SS DNA repairMRC1 RRM3 YHR031C 3 SL SL DNA replicationMRC1 CTF8 YHR191C 2 SL SL Chromatin/chromosome structureMRC1 HPR5 YJL092W 0 SL SS DNA repairMRC1 POL32 YJR043C 3 SL SL DNA replicationMRC1 RAD27 YKL113C 0 SS SS DNA repairMRC1 RAD52 YML032C 1 SS DNA repairMRC1 CSM3 YMR048W 0 SS SS MeiosisMRC1 CTF18 YMR078C 0 SL Chromatin/chromosome structureMRC1 SGS1 YMR190C 3 SS SS DNA repairMRC1 CIK1 YMR198W 0 SL SL MitosisMRC1 RAD50 YNL250W 1 SS DNA repairMRC1 TOF1 YNL273W 3 SS SS DNA repairMRC1 HTZ1 YOL012C 1 SS Chromatin/chromosome structureMRC1 YOR024W YOR024W 2 SS SS UnknownMRC1 HST3 YOR025W 3 SL SS Chromatin/chromosome structureMRC1 ELG1 YOR144C 1 SS DNA repairMRC1 RAD17 YOR368W 3 SL SS DNA repairMRC1 DDC1 YPL194W 2 SL SS DNA repairMRC1 CTF4 YPR135W 3 SL SL Chromatin/chromosome structure

Page 83: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

MRC1 KAR3 YPR141C 0 SL SL MitosisTOF1 NUP60 YAR002w 0 SL Nuclear-cytoplasmic transportTOF1 UMP1 YBR173C 2 SL Protein degradationTOF1 DCC1 YCL016C 3 SL SL Chromatin/chromosome structureTOF1 MRC1 YCL061C 3 SS DNA repairTOF1 RAD55 YDR076W 1 SS DNA repairTOF1 RAD9 YDR217C 2 SS SS DNA repairTOF1 IPK1 YDR315C 2 SL Lipid metabolismTOF1 RAD23 YEL037C 1 SS DNA repairTOF1 BIM1 YER016W 3 SL MitosisTOF1 RAD24 YER173W 3 SL SS DNA repairTOF1 RAD54 YGL163C 1 SS DNA repairTOF1 CTF8 YHR191C 2 SL SL Chromatin/chromosome structureTOF1 POL32 YJR043C 2 SL SL DNA replicationTOF1 RAD27 YKL113C 2 SL DNA repairTOF1 RAD5 YLR032W 1 SS DNA repairTOF1 TOP3 YLR234W 3 SL Chromatin/chromosome structureTOF1 MEC3 YLR288C 3 SL DNA repairTOF1 RAD52 YML032C 0 SS DNA repairTOF1 CTF18 YMR078C 0 SL SL Chromatin/chromosome structureTOF1 CIK1 YMR198W 2 SL MitosisTOF1 HTZ1 YOL012C 1 SS Chromatin/chromosome structureTOF1 ELG1 YOR144C 1 SS DNA repairTOF1 RAD17 YOR368W 2 SS SS DNA repairTOF1 DDC1 YPL194W 3 SL DNA repairTOF1 CTF4 YPR135W 3 SL SL Chromatin/chromosome structureTOF1 KAR3 YPR141C 3 SL MitosisELG1 YBR094W YBR094W 3 SS Unknown Bellaoui, 2003ELG1 MMS4 YBR098W 3 SS DNA repair Bellaoui, 2003ELG1 YBR099C YBR099C 3 SL Unknown Bellaoui, 2003ELG1 MMS4 YBR100W 2 SS DNA repair Bellaoui, 2003ELG1 MRC1 YCL061C 3 SS DNA repair Bellaoui, 2003ELG1 HEX3 YDL013W 0 SS Meiosis Bellaoui, 2003ELG1 BRE1 YDL074C 2 SS Chromatin/chromosome stucture Bellaoui, 2003ELG1 RAD57 YDR004W 3 SS DNA repair Bellaoui, 2003ELG1 RAD55 YDR076W 3 SS DNA repair Bellaoui, 2003ELG1 SWR1 YDR334W 3 SS Unknown Bellaoui, 2003ELG1 XRS2 YDR369C 2 SL DNA repair Bellaoui, 2003ELG1 MUS81 YDR386W 3 SL DNA repair Bellaoui, 2003ELG1 BIM1 YER016W 2 SS Mitosis Bellaoui, 2003ELG1 RAD51 YER095W 3 SS DNA repair Bellaoui, 2003ELG1 SLX8 YER116C 3 SS DNA repair Bellaoui, 2003ELG1 RAD24 YER173W 0 SS DNA repair Bellaoui, 2003ELG1 RAD54 YGL163C 3 SS DNA repair Bellaoui, 2003ELG1 YOR1 YGR281W 2 SS Small molecule transport Bellaoui, 2003ELG1 HPR5 YJL092W 2 SS DNA repair Bellaoui, 2003ELG1 POL32 YJR043C 3 SL DNA replication Bellaoui, 2003ELG1 RAD27 YKL113C 2 SS DNA repair Bellaoui, 2003ELG1 RTT109 YLL002W 3 SS DNA repair Bellaoui, 2003ELG1 TOP3 YLR234W 3 SS Chromatin/chromosome structure Bellaoui, 2003ELG1 YLR235C YLR235C 3 SS Unknown Bellaoui, 2003ELG1 RAD52 YML032C 3 SS DNA repair Bellaoui, 2003ELG1 SGS1 YMR190C 0 SS DNA repair Bellaoui, 2003ELG1 MRE11 YMR224C 0 SL DNA repair Bellaoui, 2003ELG1 RAD50 YNL250W 2 SL DNA repair Bellaoui, 2003ELG1 TOF1 YNL273W 2 SS DNA repair Bellaoui, 2003ELG1 MID1 YNL291C 3 SS Small molecule transport Bellaoui, 2003ELG1 BRE5 YNR051C 2 SS Unknown Bellaoui, 2003ELG1 CHL1 YPL008W 0 SS Chromatin/chromosome structure Bellaoui, 2003ELG1 CTF4 YPR135W 3 SL Chromatin/chromosome structure Bellaoui, 2003ELG1 KAR3 YPR141C 3 SS Mitosis Bellaoui, 2003

Page 84: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

POL32 LTE1 YAL024C 2 SL Cell cycle controlPOL32 MSI1 YBR195C 0 SS Chromatin/chromosome structurePOL32 DCC1 YCL016C 0 SS Chromatin/chromosome structurePOL32 MRC1 YCL060C 3 SL DNA repairPOL32 RAD55 YDR076W 2 SS DNA repairPOL32 RAD9 YDR217C 3 SL DNA repairPOL32 MNN10 YDR245W 2 SL Protein modificationPOL32 VID21 YDR359C 2 SL UnknownPOL32 XRS2 YDR369C 2 SL DNA repairPOL32 RAD51 YER095W 2 SS DNA repairPOL32 UBP3 YER151C 2 SS Protein modificationPOL32 RAD24 YER173W 2 SS DNA repairPOL32 RAD54 YGL163C 3 SS DNA repairPOL32 RAD27 YKL113C 3 SL DNA repairPOL32 TOP3 YLR234W 2 SL Chromatin/chromosome structurePOL32 YLR235C YLR235C 3 SL UnknownPOL32 ARC18 YLR370C 3 SS Cell polarityPOL32 RAD52 YML032C 3 SL DNA repairPOL32 CSM3 YMR048W 3 SL MeiosisPOL32 CTF18 YMR078C 0 SL Chromatin/chromosome structurePOL32 YDJ1 YNL064C 3 SL Mitochondrion organization and biogenesisPOL32 RAD50 YNL250W 2 SL SL DNA repairPOL32 TOF1 YNL273W 2 SL SL DNA repairPOL32 RAD17 YOR368W 2 SS DNA repairPOL32 NCE4 YPL024W 2 SL Cell wall organization and biogenesisPOL32 DDC1 YPL194W 3 SS DNA repairPOL32 CTF4 YPR135W 2 SS Chromatin/chromosome structureTOP1 MMS4 YBR098W 1 SS DNA repairTOP1 PAT1 YCR077C 2 SL Chromatin/chromosome structureTOP1 YDR249C YDR249C 2 SS UnknownTOP1 ASF1 YJL115W 1 SS Chromatin/chromosome structureTOP1 MRP17 YKL003C 2 SL Protein synthesisTOP1 TOP3 YLR234W 1 SL Chromatin/chromosome structureTOP1 YLR235C YLR235C 0 SL UnknownTOP1 RAD52 YML032C 0 SS DNA repairTOP1 MFT1 YML062C 2 SL Mitochondrion organization and biogenesisTOP1 SGS1 YMR190C 0 SL DNA repairTOP1 MRE11 YMR224C 1 SL DNA repairTOP1 RAD50 YNL250W 1 SL DNA repairTOP1 BRE5 YNR051C 0 SL UnknownTOP1 HMS1 YOR032C 1 SL Pol II transcriptionTOP1 EXO1 YOR033C 3 SL DNA repairTOP1 YOR044W YOR044W 2 SS UnknownTOP1 TOM6 YOR045W 2 SS Mitochondrion organization and biogenesisTOP1 NCE4 YPL024W 2 SL Cell wall organization and biogenesisTOP1 MCM16 YPR046W 1 SS Chromatin/chromosome structureCDC2-1 YBR094W YBR094W 2 SL UnknownCDC2-1 MMS4 YBR098W 1 SL DNA repairCDC2-1 MRC1 YCL060C 0 SL DNA repairCDC2-1 RAD57 YDR004W 1 SL DNA repairCDC2-1 RAD24 YER173W 3 SL DNA repairCDC2-1 UBP6 YFR010W 1 SL Protein modificationCDC2-1 POL32 YJR043C 3 SL DNA replicationCDC2-1 CSM3 YMR048W 1 SL MeiosisCDC2-1 YMR075C-A YMR075C-A 1 SS UnknownCDC2-1 GAS1 YMR307W 2 SL Cell wall organization and biogenesisCDC2-1 TOF1 YNL273W 0 SL DNA repairCDC2-1 MID1 YNL291C 0 SL Small molecule transportCDC2-1 MCK1 YNL307C 3 SL MeiosisCDC2-1 TRM10 YOL093W 0 SL tRNA methylationCDC2-1 RAD17 YOR368W 2 SL DNA repair

Page 85: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

CDC2-1 DDC1 YPL194W 2 SL DNA repairCDC45-1 LTE1 YAL024C 0 SL Cell cycle controlCDC45-1 HIR1 YBL008W 2 SS Chromatin/chromosome structureCDC45-1 CSS2 YBR036C 2 SS Small molecule transportCDC45-1 MMS4 YBR098W 0 SS DNA repairCDC45-1 MSI1 YBR195C 0 SS Chromatin/chromosome structureCDC45-1 HPC2 YBR215W 2 SL Pol II transcriptionCDC45-1 AOR1 YBR231C 2 SL SL UnknownCDC45-1 CHK1 YBR274W 0 SL SL DNA repairCDC45-1 YBR277C YBR277C 2 SL SL UnknownCDC45-1 DPB3 YBR278W 2 SL SL DNA replicationCDC45-1 DCC1 YCL016C 2 SL SL Chromatin/chromosome structureCDC45-1 MRC1 YCL060C 2 SL SL DNA repairCDC45-1 PAT1 YCR077C 0 SL SL Chromatin/chromosome structureCDC45-1 CSM1 YCR086W 2 SL SL MeiosisCDC45-1 NHP10 YDL002C 0 SL SL UnknownCDC45-1 FYV3 YDL151C 2 SS UnknownCDC45-1 RAD57 YDR004W 2 SS DNA repairCDC45-1 DPB4 YDR121W 0 SL DNA replicationCDC45-1 SWI5 YDR146C 2 SL Pol II transcriptionCDC45-1 RAD9 YDR217C 0 SL DNA repairCDC45-1 RTT103 YDR289C 2 SL UnknownCDC45-1 XRS2 YDR369C 0 SL DNA repairCDC45-1 VPS72 YDR485C 2 SL Vesicular transportCDC45-1 GIM4 YEL003W 0 SL Cell structureCDC45-1 HAT2 YEL056W 0 SL Chromatin/chromosome structureCDC45-1 NPR2 YEL062W 2 SL Small molecule transportCDC45-1 SWI4 YER111C 0 SL Cell cycle controlCDC45-1 SPT2 YER161C 2 SL Chromatin/chromosome stuctureCDC45-1 RAD24 YER173W 0 SL DNA repairCDC45-1 FAB1 YFR019W 2 SL Lipid metabolismCDC45-1 MAD1 YGL086W 2 SL MitosisCDC45-1 SOH1 YGL127C 2 SL DNA repairCDC45-1 ARO2 YGL148W 2 SL Amino-acid metabolismCDC45-1 NUT1 YGL151W 2 SL Pol II transcriptionCDC45-1 RAD54 YGL163C 0 SL DNA repairCDC45-1 KEM1 YGL173C 2 SL RNA processingCDC45-1 RTF1 YGL244W 3 SL Pol II transcriptionCDC45-1 RMD11 YHL023C 2 SL MeiosisCDC45-1 RRM3 YHR031C 2 SL DNA replicationCDC45-1 VMA10 YHR039C-B 2 SL Small molecule transportCDC45-1 STB5 YHR178W 2 SL Pol II transcriptionCDC45-1 CTF8 YHR191C 2 SL Chromatin/chromosome structureCDC45-1 APQ12 YIL040W 2 SL UnknownCDC45-1 IMP2' YIL154C 2 SL Carbohydrate metabolismCDC45-1 MAD2 YJL030W 2 SL MitosisCDC45-1 HPR5 YJL092W 0 SL DNA repairCDC45-1 ASF1 YJL115W 2 SL Chromatin/chromosome structureCDC45-1 LSM1 YJL124C 0 SL RNA turnoverCDC45-1 POL32 YJR043C 0 SL DNA replicationCDC45-1 BFA1 YJR053W 3 SL MitosisCDC45-1 YJR070C YJR070C 2 SL UnknownCDC45-1 SOD1 YJR104C 0 SL Cell stressCDC45-1 HIR3 YJR140C 0 SL Pol II transcriptionCDC45-1 SIS2 YKR072C 2 SL Cell stressCDC45-1 RTT109 YLL002W 2 SL DNA repairCDC45-1 SPT8 YLR055C 3 SL Chromatin/chromosome structureCDC45-1 TOP3 YLR234W 2 SL Chromatin/chromosome structureCDC45-1 YLR235C YLR235C 2 SL UnknownCDC45-1 SEC22 YLR268W 3 SL Vesicular transportCDC45-1 MEC3 YLR288C 0 SL DNA repair

Page 86: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

CDC45-1 RAD52 YML032C 0 SL DNA repairCDC45-1 GIM5 YML094W 2 SS SS Cell structureCDC45-1 SUB1 YMR039C 0 SS Pol II transcriptionCDC45-1 CSM3 YMR048W 2 SS MeiosisCDC45-1 BUB2 YMR055C 0 SS MitosisCDC45-1 CTF18 YMR078C 0 SL Chromatin/chromosome structureCDC45-1 YMR166C YMR166C 2 SS TransportCDC45-1 SCS7 YMR272C 2 SS Lipid metabolismCDC45-1 IES2 YNL215W 2 SS UnknownCDC45-1 TOF1 YNL273W 2 SS DNA repairCDC45-1 RIM21 YNL294C 2 SS UnknownCDC45-1 TRF5 YNL299W 0 SS Chromatin/chromosome structureCDC45-1 TOP1 YOL006C 2 SS Chromatin/chromosome structureCDC45-1 HTZ1 YOL012C 3 SS Chromatin/chromosome structureCDC45-1 MET22 YOL064C 2 SS Amino-acid metabolismCDC45-1 YOR024W YOR024W 2 SS UnknownCDC45-1 HST3 YOR025W 0 SS Chromatin/chromosome structureCDC45-1 DFG16 YOR030W 2 SS DifferentiationCDC45-1 HIR2 YOR038C 2 SS Pol II transcriptionCDC45-1 WHI2 YOR043W 2 SS Cell cycle controlCDC45-1 LEO1 YOR123C 2 SS Chromatin/chromosome structureCDC45-1 RAD17 YOR368W 2 SS DNA repairCDC45-1 HAT1 YPL001W 0 SS Chromatin/chromosome structureCDC45-1 NCE4 YPL024W 2 SS Cell wall organization and biogenesisCDC45-1 LGE1 YPL055C 2 SS Cell cycle controlCDC45-1 GON5 YPL183W-A 2 SS Protein synthesisCDC45-1 DDC1 YPL194W 0 SS DNA repairCDC45-1 BRR1 YPR057W 3 SS RNA processingCDC45-1 MED1 YPR070W 2 SS Chromatin/chromosome structureCDC45-1 CLB5 YPR120C 0 SL Cell cycle controlCDC45-1 CTF4 YPR135W 2 SL Chromatin/chromosome structureCDC45-1 KAR3 YPR141C 2 SS MitosisCDC7-1 HIR1 YBL008W 2 SS Chromatin/chromosome structureCDC7-1 CHK1 YBR274W 3 SS DNA repairCDC7-1 DCC1 YCL016C 2 SS Chromatin/chromosome structureCDC7-1 RPS14A YCR031C 3 SS Protein synthesisCDC7-1 FEN1 YCR034W 2 SS Lipid metabolismCDC7-1 FYV3 YDL151C 2 SS UnknownCDC7-1 RAD9 YDR217C 3 SS DNA repairCDC7-1 ESC2 YDR363W 3 SS Chromatin/chromosome structureCDC7-1 RAD24 YER173W 3 SS DNA repairCDC7-1 CKB1 YGL019W 3 SS Cell cycle controlCDC7-1 MAD1 YGL086W 3 SS MitosisCDC7-1 YGL250W YGL250W 2 SS UnknownCDC7-1 RTT107 YHR154W 2 SS Chromatin/chromosome structureCDC7-1 CTF8 YHR191C 3 SS Chromatin/chromosome structureCDC7-1 CKA1 YIL035C 3 SS Cell cycle controlCDC7-1 MAD2 YJL030W 3 SS MitosisCDC7-1 LAS21 YJL062W 2 SS Lipid metabolismCDC7-1 TIF2 YJL138C 2 SS Protein synthesisCDC7-1 CPR7 YJR032W 2 SS Protein foldingCDC7-1 BFA1 YJR053W 2 SS MitosisCDC7-1 YJR070C YJR070C 2 SS UnknownCDC7-1 HIR3 YJR140C 2 SS Pol II transcriptionCDC7-1 YKL056C YKL056C 2 SS UnknownCDC7-1 HSL1 YKL101W 3 SS Cell cycle controlCDC7-1 TIF1 YKR059W 2 SS Protein synthesisCDC7-1 SPT8 YLR055C 2 SS Chromatin/chromosome structureCDC7-1 TOP3 YLR234W 3 SS Chromatin/chromosome structureCDC7-1 YLR235C YLR235C 2 SS UnknownCDC7-1 MEC3 YLR288C 0 SS DNA repair

Page 87: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

CDC7-1 ORM2 YLR350W 2 SS Cell wall organization and biogenesisCDC7-1 TSR2 YLR435W 2 SS UnknownCDC7-1 PPZ1 YML016C 2 SS Signal transductionCDC7-1 RAD52 YML032C 2 SS DNA repairCDC7-1 BUB2 YMR055C 2 SS MitosisCDC7-1 CTF18 YMR078C 0 SS Chromatin/chromosome structureCDC7-1 MUB1 YMR100W 3 SS Cell polarityCDC7-1 MLH1 YMR167W 2 SS DNA repairCDC7-1 SGS1 YMR190C 3 SS DNA repairCDC7-1 IRA2 YOL081W 2 SS Signal transductionCDC7-1 STI1 YOR027W 2 SS Protein foldingCDC7-1 CKB2 YOR039W 2 SS Cell cycle controlCDC7-1 PDE2 YOR360C 2 SS Signal transductionCDC7-1 RAD17 YOR368W 3 SS DNA repairCDC7-1 DDC1 YPL194W 2 SS DNA repairCDC7-1 CLB2 YPR119W 2 SS Cell cycle controlDBF4 HIR1 YBL008W 0 SS Chromatin/chromosome structureDBF4 HPC2 YBR215W 2 SS Pol II transcriptionDBF4 CHK1 YBR274W 0 SS DNA repairDBF4 DCC1 YCL016C 2 SS Chromatin/chromosome structureDBF4 RPS14A YCR031C 3 SS Protein synthesisDBF4 YDL062W YDL062W 2 SS UnknownDBF4 RAD9 YDR217C 2 SS DNA repairDBF4 ESC2 YDR363W 0 SS Chromatin/chromosome structureDBF4 RAD24 YER173W 3 SS DNA repairDBF4 BMH1 YER177W 3 SS DifferentiationDBF4 RSM23 YGL129C 2 SS Protein synthesisDBF4 KEM1 YGL173C 2 SS RNA processingDBF4 PAC10 YGR078C 3 SS Cell structureDBF4 BUB1 YGR188C 0 SL MitosisDBF4 RTT107 YHR154W 3 SS Chromatin/chromosome structureDBF4 STB5 YHR178W 2 SS Pol II transcriptionDBF4 CTF8 YHR191C 3 SS Chromatin/chromosome structureDBF4 MET18 YIL128W 2 SS Pol II TranscriptionDBF4 HIR3 YJR140C 3 SS Pol II transcriptionDBF4 TIF1 YKR059W 2 SS Protein synthesisDBF4 TOP3 YLR234W 0 SS Chromatin/chromosome structureDBF4 YLR235C YLR235C 0 SS UnknownDBF4 MEC3 YLR288C 3 SS DNA repairDBF4 MMS22 YLR320W 2 SS UnknownDBF4 GIM5 YML094W 2 SS Cell structureDBF4 VAN1 YML115C 2 SS Protein modificationDBF4 GIM3 YNL153C 3 SS Cell structureDBF4 IRA2 YOL081W 0 SS Signal transductionDBF4 STI1 YOR027W 2 SS Protein foldingDBF4 RAD17 YOR368W 3 SS DNA repairDBF4 NCE4 YPL024W 2 SS Cell wall organization and biogenesisDBF4 CTF4 YPR135W 0 SS Chromatin/chromosome structureDDC1 DCC1 YCL016C 0 SS Chromatin/chromosome structureDDC1 MRC1 YCL061C 3 SL DNA repairDDC1 YDL033C YDL033C 2 SS UnknownDDC1 HTA1 YDR225W 0 SS Chromatin/chromosome structureDDC1 POL32 YJR043C 3 SL DNA replicationDDC1 RAD27 YKL113C 0 SL DNA repairDDC1 LYS7 YMR038C 2 SL Amino-acid metabolismDDC1 CSM3 YMR048W 2 SS MeiosisDDC1 CTF18 YMR078C 0 SL Chromatin/chromosome structureDDC1 TOF1 YNL273W 3 SS DNA repairDDC1 CLA4 YNL298W 0 SS Cell polarityDDC1 HXT17 YNR072W 3 SL Small molecule transportDDC1 YME1 YPR024W 3 SL Mitochondrion organization and biogenesis

Page 88: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

DDC1 KAR3 YPR141C 0 SS MitosisRAD9 DCC1 YCL016C 0 SS Chromatin/chromosome structureRAD9 MRC1 YCL060C 3 SL DNA repairRAD9 YDL162C YDL162C 3 SS UnknownRAD9 YHL029C YHL029C 0 SS UnknownRAD9 CTF8 YHR191C 0 SL Chromatin/chromosome structureRAD9 POL32 YJR043C 3 SL DNA replicationRAD9 RAD27 YKL113C 0 SS DNA repairRAD9 SEC22 YLR268W 2 SS Vesicular transportRAD9 CSM3 YMR048W 2 SS MeiosisRAD9 CTF18 YMR078C 0 SL Chromatin/chromosome structureRAD9 GIM3 YNL153C 2 SS Cell structureRAD9 TOF1 YNL273W 3 SL DNA repairRAD24 MRC1 YCL060C 3 SS DNA repairRAD24 SOD1 YJR104C 1 SS Cell stressRAD24 DOA1 YKL213C 1 SS Protein degradationRAD24 CTF18 YMR078C 0 SL Chromatin/chromosome structureRAD24 TOF1 YNL273W 3 SS DNA repairRAD50 DEP1 YAL013w 0 SL Lipid metabolismRAD50 NUP60 YAR002w 0 SL Nuclear-cytoplasmic transportRAD50 SWD1 YAR003W 2 SS Chromatin/chromosome structureRAD50 SWD3 YBR175W 0 SL Chromatin/chromosome structureRAD50 DCC1 YCL016c 0 SL Chromatin/chromosome structureRAD50 MRC1 YCL060C 2 SL DNA repairRAD50 CSM1 YCR086W 0 SL MeiosisRAD50 BRE1 YDL074c 0 SS Chromatin/chromosome stuctureRAD50 YDL162C YDL162C 3 SL UnknownRAD50 SWM1 YDR260C 2 SS MeiosisRAD50 RNH202 YDR279W 2 SS UnknownRAD50 ESC2 YDR363W 0 SS Chromatin/chromosome structureRAD50 NPR2 YEL062W 3 SL Small molecule transportRAD50 BIM1 YER016W 2 SS MitosisRAD50 UBP6 YFR010W 3 SL Protein modificationRAD50 SLT2 YHR030c 0 SL Cell wall organization and biogenesisRAD50 RRM3 YHR031C 0 SL DNA replicationRAD50 RTT107 YHR154W 0 SL Chromatin/chromosome structureRAD50 CTF8 YHR191C 0 SL Chromatin/chromosome structureRAD50 RTT101 YJL047c 0 SS Protein modificationRAD50 BCK1 YJL095W 0 SS Cell wall organization and biogenesisRAD50 ASF1 YJL115W 0 SL Chromatin/chromosome structureRAD50 POL32 YJR043C 2 SL DNA replicationRAD50 HSL1 YKL101W 0 SS Cell cycle controlRAD50 RAD27 YKL113C 2 SL DNA repairRAD50 BRE2 YLR015W 2 SL Chromatin/chromosome structureRAD50 RAD5 YLR032W 0 SS DNA repairRAD50 VID22 YLR373c 0 SL Vacuolar organization and biogenesisRAD50 TSA1 YML028W 3 SL Cell stressRAD50 YML095C-A YML095C-A 0 SS UnknownRAD50 VAN1 YML115C 2 SL Protein modificationRAD50 LYS7 YMR038C 0 SL Amino-acid metabolismRAD50 CTF18 YMR078C 0 SL Chromatin/chromosome structureRAD50 MLS1 YNL117w 0 SL Lipid metabolismRAD50 MID1 YNL291C 2 SL Small molecule transportRAD50 CLA4 YNL298W 3 SL Cell polarityRAD50 TOP1 YOL006C 0 SS Chromatin/chromosome structureRAD50 ELG1 YOR144C 2 SL DNA repairRAD50 RLF2 YPR018W 0 SL Chromatin/chromosome structureRAD50 CLB2 YPR119W 2 SL Cell cycle controlRAD50 CTF4 YPR135w 0 SL Chromatin/chromosome structureRAD52 UMP1 YBR173C 3 SL Protein degradationRAD52 DCC1 YCL016C 0 SS Chromatin/chromosome structure

Page 89: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

RAD52 SIT4 YDL047W 3 SL Cell wall organization and biogenesisRAD52 YDL162C YDL162C 3 SL UnknownRAD52 PMR1 YGL167C 3 SL Small molecule transportRAD52 HUR1 YGL168W 2 SL UnknownRAD52 KEM1 YGL173C 3 SL RNA processingRAD52 POL32 YJR043C 2 SL DNA replicationRAD52 RAD27 YKL113C 3 SL DNA repairRAD52 LYS7 YMR038C 2 SL Amino-acid metabolismRAD52 CTF18 YMR078C 0 SS Chromatin/chromosome structureRAD52 ELG1 YOR144C 3 SL DNA repairCDC8 MMS4 YBR098w 0 SS DNA repairCDC8 MRC1 YCL060C 3 SS DNA repairCDC8 CSM1 YCR086W 2 SS MeiosisCDC8 YDR438W YDR438W 2 SS UnknownCDC8 ECM11 YDR446W 2 SS Cell wall organization and biogenesisCDC8 PPN1 YDR452W 2 SL Phosphate metabolismCDC8 TSA2 YDR453C 2 SL Cell stressCDC8 YDR458C YDR458C 2 SL UnknownCDC8 PKH1 YDR490C 2 SS EndocytosisCDC8 BCK2 YER167W 2 SS Cell cycle controlCDC8 RAD24 YER173W 2 SS DNA repairCDC8 SWF3 YGL020C 3 SS UnknownCDC8 KEM1 YGL173C 2 SL RNA processingCDC8 STB5 YHR178w 0 SL Pol II transcriptionCDC8 PET191 YJR034W 3 SL Energy generationCDC8 IXR1 YKL032c 0 SS DNA repairCDC8 YKL098W YKL098W 3 SS UnknownCDC8 RAD27 YKL113C 3 SS DNA repairCDC8 APN1 YKL114C 3 SL DNA repairCDC8 TOP3 YLR234W 2 SL Chromatin/chromosome structureCDC8 YLR235C YLR235C 2 SL UnknownCDC8 SEC22 YLR268W 3 SL Vesicular transportCDC8 SGS1 YMR190C 2 SS DNA repairCDC8 CIK1 YMR198W 0 SS MitosisCDC8 MGS1 YNL218W 2 SS DNA replicationCDC8 URE2 YNL229c 0 SL Amino-acid metabolismCDC8 ZWF1 YNL241C 2 SL Carbohydrate metabolismCDC8 TRF5 YNL299W 2 SL Chromatin/chromosome structureCDC8 ISW2 YOR304W 3 SS Chromatin/chromosome strucutreCDC8 DDC1 YPL194W 2 SS DNA repairMMS4 ESC2 YDR363W 2 SS Chromatin/chromosome structureMMS4 XRS2 YDR369C 1 SS DNA repairMMS4 RAD27 YKL113c 0 SL DNA repairMMS4 TOP3 YLR234W 3 SL Chromatin/chromosome structureMMS4 YLR235C YLR235C 3 SL UnknownMMS4 VID22 YLR373C 2 SS Vacuolar organization and biogenesisMMS4 SGS1 YMR190C 3 SL DNA repairMMS4 NCE4 YPL024W 3 SL Cell wall organization and biogenesisMUS81 RAD27 YKL113c 0 SL DNA repairMUS81 TOP3 YLR234W 2 SL Chromatin/chromosome structureMUS81 YLR235C YLR235C 2 SL UnknownMUS81 VID22 YLR373C 2 SS Vacuolar organization and biogenesisMUS81 SGS1 YMR190C 3 SL DNA repairMUS81 ELG1 YOR144C 2 SS DNA repairMUS81 NCE4 YPL024W 3 SL Cell wall organization and biogenesisYBR094w SOY YBR194W 2 SL UnknownYBR094w CSM1 YCR086W 0 SS MeiosisYBR094w YDL162C YDL162C 2 SS UnknownYBR094w ESC2 YDR363W 3 SL Chromatin/chromosome structureYBR094w ISC1 YER019W 1 SS Lipid metabolismYBR094w YEN1 YER041W 3 SS DNA repair

Page 90: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

YBR094w SOH1 YGL127C 1 SS DNA repairYBR094w ASF1 YJL115W 0 SS Chromatin/chromosome structureYBR094w POL32 YJR043C 2 SS DNA replicationYBR094w TOP3 YLR234W 2 SL Chromatin/chromosome structureYBR094w VID22 YLR373C 2 SS Vacuolar organization and biogenesisYBR094w TSA1 YML028W 3 SL Cell stressYBR094w LYS7 YMR038C 0 SS Amino-acid metabolismYBR094w SGS1 YMR190C 2 SL DNA repairYBR094w GIM3 YNL153C 1 SS Cell structureYBR094w MON2 YNL297C 2 SL Vacuolar organization and biogenesisYBR094w RRP6 YOR001W 1 SS RNA processingYBR094w ELG1 YOR144C 3 SL DNA repairYBR094w NCE4 YPL024W 3 SL Cell wall organization and biogenesisHST1 ESC2 YDR363W 1 SS Chromatin/chromosome structureHST1 WHI2 YOR043W 2 SS Cell cycle controlHST3 MRC1 YCL060C 2 SL DNA repairHST3 HST4 YDR191W 2 SL Chromatin/chromosome structureHST3 POL32 YJR043C 0 SS DNA replicationHST3 RAD27 YKL113C 2 SL DNA repairHST3 YLR235C YLR235C 0 SL UnknownHST3 YML095C-A YML095C-A 0 SS UnknownHST3 SGS1 YMR190C 1 SS DNA repairHST3 CIK1 YMR198W 2 SL MitosisHST3 YOR082C YOR082C 1 SS UnknownESC2 NUP60 YAR002W 2 SL Nuclear-cytoplasmic transportESC2 SWD1 YAR003W 1 SL Chromatin/chromosome structureESC2 YBR094W YBR094W 3 SL UnknownESC2 MMS4 YBR098W 3 SL DNA repairESC2 YBR099C YBR099C 0 SL UnknownESC2 YBR174C YBR174C 0 SL UnknownESC2 SLX1 YBR228W 3 SL DNA repairESC2 SRO9 YCL037C 0 SL Protein synthesisESC2 RPN4 YDL020C 1 SL Protein degradationESC2 RNH202 YDR279W 1 SL SS UnknownESC2 MUS81 YDR386W 3 SL DNA repairESC2 UBP6 YFR010W 0 SS Protein modificationESC2 YGR071C YGR071C 0 SL SS UnknownESC2 UPF3 YGR072W 3 SL RNA turnoverESC2 RRM3 YHR031C 1 SL DNA replicationESC2 NMD2 YHR077C 3 SL RNA turnoverESC2 WSS1 YHR134W 1 SS DNA repairESC2 THP2 YHR167W 0 SS RecombinationESC2 RPL34B YIL052C 0 SS Protein synthesisESC2 HPR5 YJL092W 0 SS DNA repairESC2 SWI3 YJL176C 2 SL Chromatin/chromosome structureESC2 POL32 YJR043C 2 SS DNA replicationESC2 HIR3 YJR140C 0 SS SS Pol II transcriptionESC2 SLX4 YLR135W 3 SL DNA repairESC2 RNH203 YLR154C 1 SS SS UnknownESC2 YLR235C YLR235C 0 SL UnknownESC2 VID22 YLR373C 3 SL Vacuolar organization and biogenesisESC2 YLR374C YLR374C 3 SS SS UnknownESC2 MSC1 YML128C 1 SS UnknownESC2 NAM7 YMR080C 2 SL RNA turnoverESC2 SGS1 YMR190C 1 SS DNA repairESC2 RNH35 YNL072W 0 SS DNA replicationESC2 INP52 YNL106C 2 SL Lipid metabolismESC2 MGS1 YNL218W 0 SS DNA replicationESC2 TOP1 YOL006C 0 SS Chromatin/chromosome structureESC2 SKI7 YOR076C 0 SL RNA turnoverESC2 LEO1 YOR123C 0 SS Chromatin/chromosome structure

Page 91: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

ESC2 RIS1 YOR191W 0 SL Chromatin/chromosome structureESC2 PUS7 YOR243C 0 SS RNA processingESC2 NCE4 YPL024W 0 SL Cell wall organization and biogenesisESC2 SUR1 YPL057C 0 SS Lipid metabolismESC2 RPL21B YPL079W 0 SS Protein synthesisRTT107 RMD7 YER083C 2 SS Cell wall organization and biogenesisRTT107 PMR1 YGL167C 1 SS Small molecule transportRTT107 HUR1 YGL168W 1 SS UnknownRTT107 RRM3 YHR031C 2 SS DNA replicationRTT107 ZAP1 YJL056C 2 SS Pol II transcriptionRTT107 SOD1 YJR104C 0 SS Cell stressRTT107 TOP3 YLR234W 2 SS Chromatin/chromosome structureRTT107 YLR235C YLR235C 3 SS UnknownRTT107 VID22 YLR373C 0 SS Vacuolar organization and biogenesisRTT107 IMP2 YMR035W 0 SS Mitochondrion organization and biogenesisRTT107 SGS1 YMR190C 0 SS DNA repairRTT107 GAL11 YOL051W 3 SS Carbohydrate metabolismRTT107 NCE4 YPL024W 3 SS Cell wall organization and biogenesisRAS2 PDR17 YNL264C 1 SL Vesicular transportRAS2 RAS1 YOR101W 3 SL Signal transductionRAS2 YNL063W YNL063W 0 SS UnknownRAS2 COX16 YJL003W 0 SS Energy generationALG6 PMT2 YAL023C 3 SL SS Protein modificationALG6 PMT1 YDL095W 2 SS SS Protein modificationALG6 YDL096C YDL096C 2 SS SS UnknownALG6 RPO41 YFL036W 3 SL SL Mitochondrion organization and biogenesisALG6 OST5 YGL226C-A 3 SL SL Protein modificationALG6 OST3 YOR085W 3 SL SL Protein modificationCHS1 DEP1 YAL013W 3 SS Lipid metabolismCHS1 PEX22 YAL055W 2 SS UnknownCHS1 ECM21 YBL101C 3 SS Cell wall organization and biogenesisCHS1 PHO5 YBR093C 3 SL Phosphate metabolismCHS1 GRS1 YBR121C 2 SL Protein synthesisCHS1 TYR1 YBR166C 3 SS Amino-acid metabolismCHS1 YBR209W YBR209W 2 SL UnknownCHS1 FIG2 YCR089W 2 SS Mating responseCHS1 YDL206W YDL206W 3 SL UnknownCHS1 HBT1 YDL223C 3 SL Cell polarityCHS1 YDR248C YDR248C 2 SS UnknownCHS1 PMP3 YDR276C 2 SL Small molecule transportCHS1 YDR314C YDR314C 2 SL DNA repairCHS1 IPK1 YDR315C 3 SS Lipid metabolismCHS1 SPF1 YEL031W 2 SS Small molecule transportCHS1 YEL033W YEL033W 3 SS DifferentiationCHS1 PEA2 YER149C 2 SL Cell polarityCHS1 PDA1 YER178W 3 SS Mitochondrion organization and biogenesisCHS1 YFR045W YFR045W 3 SL TransportCHS1 YGL081W YGL081W 3 SL UnknownCHS1 CUE3 YGL110C 2 SL UnknownCHS1 EMP24 YGL200C 3 SS Vesicular transportCHS1 HAP2 YGL237C 2 SS Pol II transcriptionCHS1 VPS29 YHR012W 3 SS Vesicular transportCHS1 YIL110W YIL110W 2 SS UnknownCHS1 BCK1 YJL095W 3 SL Cell wall organization and biogenesisCHS1 RPE1 YJL121C 2 SL Carbohydrate metabolismCHS1 RPA34 YJL148W 3 SS Protein synthesisCHS1 VPS35 YJL154C 2 SS Vesicular transportCHS1 ELO1 YJL196C 2 SS Lipid metabolismCHS1 NUC1 YJL208C 3 SS RecombinationCHS1 HXT8 YJL214W 3 SL Carbohydrate metabolismCHS1 HIT1 YJR055W 2 SL Unknown

Page 92: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

CHS1 CNB1 YKL190W 3 SS Cell wall organization and biogenesisCHS1 UTH1 YKR042W 2 SS AgingCHS1 FPS1 YLL043W 2 SS TransportCHS1 PDC1 YLR044C 2 SL Carbohydrate metabolismCHS1 BUD20 YLR074C 2 SL Cell polarityCHS1 ARC18 YLR370C 2 SS Cell polarityCHS1 SKI2 YLR398C 2 SS RNA turnoverCHS1 YMR003W YMR003W 2 SL UnknownCHS1 PKR1 YMR123W 2 SS UnknownCHS1 PFK2 YMR205C 3 SS Carbohydrate metabolismCHS1 MRE11 YMR224C 2 SS DNA repairCHS1 YNL087W YNL087W 2 SL UnknownCHS1 YNL171C YNL171C 2 SS UnknownCHS1 YNL179C YNL179C 2 SL UnknownCHS1 YNL200C YNL200C 2 SL UnknownCHS1 PSY2 YNL201C 2 SL Carbohydrate metabolismCHS1 SPS19 YNL202W 2 SL Lipid metabolismCHS1 YNL203C YNL203C 2 SL UnknownCHS1 SPS18 YNL204C 2 SL MeiosisCHS1 YNL228W YNL228W 2 SS UnknownCHS1 PDR16 YNL231C 3 SS Lipid metabolismCHS1 YNL235C YNL235C 3 SS UnknownCHS1 PEX6 YNL329C 3 SL Lipid metabolismCHS1 MDM38 YOL027C 2 SS Mitochondrion organization and biogenesisCHS1 WHI2 YOR043W 3 SL Cell cycle controlCHS1 VPS5 YOR069W 2 SS Vesicular transportCHS1 VPS17 YOR132W 3 SL Vesicular transportCHS1 YOR322C YOR322C 2 SL UnknownCHS1 LGE1 YPL055C 3 SS Cell cycle controlCHS1 BEM4 YPL161C 3 SS Cell polarityCHS1 PRM3 YPL192C 2 SL Mating responseCHS1 LEA1 YPL213W 2 SS RNA splicingCHS1 CLN2 YPL256C 3 SL Cell cycle controlCHS1 YPL261C YPL261C 2 SL UnknownCHS1 YME1 YPR024W 2 SS Mitochondrion organization and biogenesisCHS1 YPR053C YPR053C 2 SS UnknownCHS3 SLA1 YBL007C 3 SS Cell polarityCHS3 EDE1 YBL047C 2 SS Vesicular transportCHS3 RPS8A YBL072C 3 SS Protein synthesisCHS3 MNN2 YBR015C 3 SS Protein modificationCHS3 MUM2 YBR057C 3 SS MeiosisCHS3 YBR077C YBR077C 3 SS UnknownCHS3 YDL032W YDL032W 2 SS UnknownCHS3 YDL033C YDL033C 2 SS UnknownCHS3 HBT1 YDL223C 3 SS Cell polarityCHS3 SAC6 YDR129C 3 SL SS Cell structureCHS3 MNN10 YDR245W 0 SL Protein modificationCHS3 RVS167 YDR388W 0 SS Cell polarityCHS3 IES6 YEL044W 3 SS Vesicular transportCHS3 SWI4 YER111C 2 SS Cell cycle controlCHS3 FAB1 YFR019W 2 SS Lipid metabolismCHS3 CDC26 YFR036W 2 SL Cell cycle controlCHS3 GUP1 YGL084C 2 SS Lipid metabolismCHS3 EMP24 YGL200C 3 SS Vesicular transportCHS3 VAM7 YGL212W 2 SS Vacuolar organization and biogenesisCHS3 DOC1 YGL240W 3 SS Cell cycle controlCHS3 PRE9 YGR135W 3 SS Protein degradationCHS3 SMI1 YGR229C 3 SL Cell wall organization and biogenesisCHS3 SLT2 YHR030C 3 SS Cell wall organization and biogenesisCHS3 BCK1 YJL095W 0 SL Cell wall organization and biogenesisCHS3 RPA34 YJL148W 2 SS Protein synthesis

Page 93: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

CHS3 OPI3 YJR073C 2 SS Lipid metabolismCHS3 ILM1 YJR118C 3 SL Energy generationCHS3 VPS24 YKL041W 0 SS Vesicular transportCHS3 SMY1 YKL079W 2 SS Cell polarityCHS3 MST1 YKL194C 3 SS Protein synthesisCHS3 VPS67 YKR020W 3 SS Vacuolar organization and biogenesisCHS3 UBI4 YLL039C 3 SS Protein degradationCHS3 CSF1 YLR087C 3 SS Cell stressCHS3 CCW12 YLR110C 3 SS Cell wall organization and biogenesisCHS3 YLR111W YLR111W 3 SS UnknownCHS3 VRP1 YLR337C 0 SL Cell polarityCHS3 KRE21 YLR338W 3 SL UnknownCHS3 FKS1 YLR342W 0 SS Cell wall organization and biogenesisCHS3 ARC18 YLR370C 2 SS Cell polarityCHS3 VAN1 YML115C 3 SS Protein modificationCHS3 TOM37 YMR060C 3 SS Mitochondrion organization and biogenesisCHS3 YTA12 YMR089C 3 SS Energy generationCHS3 ASC1 YMR116C 3 SS Protein synthesisCHS3 GAS1 YMR307W 2 SS Cell wall organization and biogenesisCHS3 TPM1 YNL079C 0 SS Cell structureCHS3 YNL171C YNL171C 3 SS UnknownCHS3 BNI1 YNL271C 2 SS Cell polarityCHS3 CLA4 YNL298W 3 SS Cell polarityCHS3 BRE5 YNR051C 3 SS UnknownCHS3 SHE4 YOR035C 0 SS DifferentiationCHS3 RPL20B YOR312C 3 SS Protein synthesisCHS3 LGE1 YPL055C 3 SS Cell cycle controlCHS3 BTS1 YPL069C 2 SS Protein modificationCHS5 SLA1 YBL007C 0 SL Cell polarityCHS5 EDE1 YBL047C 0 SS Vesicular transportCHS5 RPS8A YBL072C 0 SS Protein synthesisCHS5 ECM21 YBL101C 2 SS Cell wall organization and biogenesisCHS5 GRS1 YBR121C 3 SS Protein synthesisCHS5 AOR1 YBR231C 2 SS UnknownCHS5 DAN3 YBR301W 2 SS Cell wall organization and biogenesisCHS5 RVS161 YCR009C 0 SS Cell polarityCHS5 PAT1 YCR077C 2 SL Chromatin/chromosome structureCHS5 YDL033C YDL033C 0 SS UnknownCHS5 BRE1 YDL074C 2 SS Chromatin/chromosome stuctureCHS5 CLB3 YDL155W 3 SS Cell cycle controlCHS5 YDL206W YDL206W 3 SS UnknownCHS5 SAC6 YDR129C 0 SL Cell structureCHS5 MNN10 YDR245W 2 SL Protein modificationCHS5 LSM6 YDR378C 0 SL RNA splicingCHS5 SHE9 YDR393W 2 SS Mitochondrion organization and biogenesisCHS5 DOT1 YDR440W 2 SS Chromatin/chromosome stuctureCHS5 SWI4 YER111C 2 SS Cell cycle controlCHS5 PEA2 YER149C 3 SS Cell polarityCHS5 FAB1 YFR019W 2 SS Lipid metabolismCHS5 YFR045W YFR045W 3 SS TransportCHS5 YGL081W YGL081W 3 SS UnknownCHS5 GUP1 YGL084C 0 SS Lipid metabolismCHS5 YGL152C YGL152C 3 SL UnknownCHS5 PEX14 YGL153W 3 SL Peroxisome organization and biogenesisCHS5 EMP24 YGL200C 3 SS Vesicular transportCHS5 PRE9 YGR135W 2 SS Protein degradationCHS5 SMI1 YGR229C 0 SL Cell wall organization and biogenesisCHS5 HSE1 YHL002W 2 SS TransportCHS5 SLT2 YHR030C 2 SL Cell wall organization and biogenesisCHS5 CTK2 YJL006C 2 SS Pol II transcriptionCHS5 BCK1 YJL095W 2 SL Cell wall organization and biogenesis

Page 94: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

CHS5 RPA34 YJL148W 0 SS Protein synthesisCHS5 SWI3 YJL176C 2 SL Chromatin/chromosome structureCHS5 MNN11 YJL183W 2 SL Protein modificationCHS5 RPL14A YKL006W 2 SS Protein synthesisCHS5 UFD4 YKL010C 0 SS Protein modificationCHS5 IXR1 YKL032C 0 SS DNA repairCHS5 VPS24 YKL041W 3 SS Vesicular transportCHS5 SMY1 YKL079W 2 SS Cell polarityCHS5 VPS67 YKR020W 0 SS Vacuolar organization and biogenesisCHS5 NUP133 YKR082W 0 SS Nuclear-cytoplasmic transportCHS5 UBI4 YLL039C 3 SS Protein degradationCHS5 FPS1 YLL043W 3 SS TransportCHS5 CSF1 YLR087C 0 SS Cell stressCHS5 CCW12 YLR110C 2 SS Cell wall organization and biogenesisCHS5 YLR111W YLR111W 0 SS UnknownCHS5 SEC22 YLR268W 0 SL Vesicular transportCHS5 FKS1 YLR342W 0 SS Cell wall organization and biogenesisCHS5 ARC18 YLR370C 2 SS Cell polarityCHS5 TUS1 YLR425W 0 SS UnknownCHS5 VAN1 YML115C 2 SL Protein modificationCHS5 ASC1 YMR116C 0 SS Protein synthesisCHS5 MRE11 YMR224C 3 SS DNA repairCHS5 GAS1 YMR307W 3 SS Cell wall organization and biogenesisCHS5 PET8 YNL003C 2 SS Small molecule transportCHS5 LAT1 YNL071W 3 SS Energy generationCHS5 TPM1 YNL079C 3 SS Cell structureCHS5 YNL171C YNL171C 0 SS UnknownCHS5 CLA4 YNL298W 2 SS Cell polarityCHS5 COQ2 YNR041C 2 SS Energy generationCHS5 MDM12 YOL009C 2 SL Mitochondrion organization and biogenesisCHS5 IRA2 YOL081W 2 SS Signal transductionCHS5 VPS21 YOR089C 0 SS Vesicular transportCHS5 PDE2 YOR360C 2 SS Signal transductionCHS5 LGE1 YPL055C 0 SS Cell cycle controlCHS5 COX11 YPL132W 2 SS Energy generationCHS5 BEM4 YPL161C 3 SS Cell polarityCHS5 LEA1 YPL213W 2 SS RNA splicingCHS6 MUM2 YBR057C 2 SS MeiosisCHS6 UME6 YDR207C 2 SS MeiosisCHS6 MSN5 YDR335W 2 SS Nuclear-cytoplasmic transportCHS6 RVS167 YDR388W 2 SS Cell polarityCHS6 RPO41 YFL036W 2 SS Mitochondrion organization and biogenesisCHS6 GUP1 YGL084C 0 SS Lipid metabolismCHS6 SMI1 YGR229C 0 SL Cell wall organization and biogenesisCHS6 SLT2 YHR030C 0 SS Cell wall organization and biogenesisCHS6 IST3 YIR005W 2 SS RNA splicingCHS6 LAS21 YJL062W 0 SS Lipid metabolismCHS6 BCK1 YJL095W 0 SS Cell wall organization and biogenesisCHS6 MNN11 YJL183W 2 SL Protein modificationCHS6 ILM1 YJR118C 2 SL Energy generationCHS6 NUP133 YKR082W 0 SS Nuclear-cytoplasmic transportCHS6 UBI4 YLL039C 3 SL Protein degradationCHS6 VRP1 YLR337C 2 SL Cell polarityCHS6 KRE21 YLR338W 3 SL UnknownCHS6 FKS1 YLR342W 0 SL Cell wall organization and biogenesisCHS6 ARC18 YLR370C 0 SS Cell polarityCHS6 VAN1 YML115C 2 SL Protein modificationCHS6 YNL235C YNL235C 3 SS UnknownCHS6 CLA4 YNL298W 2 SS Cell polarityCHS6 IRA2 YOL081W 3 SS Signal transductionCHS7 SLA1 YBL007C 3 SL Cell polarity

Page 95: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

CHS7 EDE1 YBL047C 0 SS Vesicular transportCHS7 CYK3 YDL117W 0 SS CytokinesisCHS7 SAC6 YDR129C 3 SL Cell structureCHS7 MNN10 YDR245W 3 SL Protein modificationCHS7 RVS167 YDR388W 0 SS Cell polarityCHS7 RPO41 YFL036W 0 SS Mitochondrion organization and biogenesisCHS7 PRE9 YGR135W 3 SS Protein degradationCHS7 SMI1 YGR229C 3 SL Cell wall organization and biogenesisCHS7 SLT2 YHR030C 3 SL Cell wall organization and biogenesisCHS7 QDR2 YIL121W 3 SS TransportCHS7 BCK1 YJL095W 3 SL Cell wall organization and biogenesisCHS7 RPA34 YJL148W 0 SS Protein synthesisCHS7 OPI3 YJR073C 0 SS Lipid metabolismCHS7 SMY1 YKL079W 0 SS Cell polarityCHS7 NUP133 YKR082W 3 SS Nuclear-cytoplasmic transportCHS7 CCW12 YLR110C 0 SS Cell wall organization and biogenesisCHS7 YLR111W YLR111W 0 SS UnknownCHS7 VRP1 YLR337C 3 SL Cell polarityCHS7 FKS1 YLR342W 3 SL Cell wall organization and biogenesisCHS7 TUS1 YLR425W 0 SS UnknownCHS7 VAN1 YML115C 3 SL Protein modificationCHS7 TPM1 YNL079C 3 SL Cell structureCHS7 BNI1 YNL271C 3 SS Cell polarityCHS7 CLA4 YNL298W 3 SS Cell polarityCHS7 PEX6 YNL329C 3 SS Lipid metabolismCHS7 SHE4 YOR035C 3 SL DifferentiationCNE1 GUP1 YGL084C 0 SS SS Lipid metabolismCNE1 MST1 YKL194C 3 SS SS Protein synthesisCNE1 PEX1 YKL197C 2 SS SS Lipid metabolismCNE1 YDJ1 YNL064C 3 SS Mitochondrion organization and biogenesisCNE1 YNL171C YNL171C 3 SS UnknownCNE1 YNR036C YNR036C 2 SL SS UnknownCTS1 PEX6 YNL329C 2 SS Lipid metabolismDIE2 RPO41 YFL036W 2 SL Mitochondrion organization and biogenesisDIE2 OST5 YGL226C-A 2 SL Protein modificationDIE2 YGR064W YGR064W 3 SS UnknownDIE2 MDM12 YOL009C 3 SS Mitochondrion organization and biogenesisDIE2 OST3 YOR085W 3 SL Protein modificationECM15 TOM37 YMR060C 3 SS Mitochondrion organization and biogenesisERV29 TOM37 YMR060C 3 SL Mitochondrion organization and biogenesisFKS1 SLA1 YBL007C 0 SL Cell polarityFKS1 EDE1 YBL047C 2 SL Vesicular transportFKS1 SKT5 YBL061C 2 SL Cell wall organization and biogenesisFKS1 YBL062W YBL062W 2 SL UnknownFKS1 CHS3 YBR023C 2 SL Cell wall organization and biogenesisFKS1 UBC4 YBR082C 2 SS Protein degradationFKS1 GRS1 YBR121C 2 SS Protein synthesisFKS1 FEN1 YCR034W 0 SS Lipid metabolismFKS1 PTC1 YDL006W 0 SL Signal transductionFKS1 HBT1 YDL223C 2 SS Cell polarityFKS1 RGP1 YDR137W 0 SS Vesicular transportFKS1 LSM6 YDR378C 2 SS RNA splicingFKS1 RVS167 YDR388W 0 SL Cell polarityFKS1 SNF1 YDR477W 2 SS SL Carbohydrate metabolismFKS1 GNP1 YDR508C 0 SS Amino-acid metabolismFKS1 SWI4 YER111C 2 SL Cell cycle controlFKS1 UBP3 YER151C 0 SS Protein modificationFKS1 BEM2 YER155C 0 SL Cell polarityFKS1 RIM8 YGL046W 0 SS UnknownFKS1 YGL081W YGL081W 2 SS UnknownFKS1 CUE3 YGL110C 0 SS Unknown

Page 96: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

FKS1 YGL196W YGL196W 2 SS UnknownFKS1 DOC1 YGL240W 2 SS Cell cycle controlFKS1 GSC2 YGR032W 0 SL Cell wall organization and biogenesisFKS1 PEX4 YGR133W 2 SS Peroxisome organization and biogenesisFKS1 PRE9 YGR135W 0 SS Protein degradationFKS1 CCH1 YGR217W 3 SL TransportFKS1 SLT2 YHR030C 2 SL Cell wall organization and biogenesisFKS1 CHS7 YHR142W 0 SL Cell wall organization and biogenesisFKS1 RPN10 YHR200W 2 SS Pol II transcriptionFKS1 IMP2' YIL154C 2 SL Carbohydrate metabolismFKS1 YJL046W YJL046W 2 SS Protein modificationFKS1 CHS6 YJL099W 3 SL Cell wall organization and biogenesisFKS1 LSM1 YJL124C 2 SS RNA turnoverFKS1 RPS21B YJL136C 2 SS Protein synthesisFKS1 MNN11 YJL183W 2 SL Protein modificationFKS1 NUC1 YJL208C 2 SS RecombinationFKS1 HIT1 YJR055W 2 SS UnknownFKS1 ILM1 YJR118C 2 SS Energy generationFKS1 IXR1 YKL032C 2 SS DNA repairFKS1 ELM1 YKL048C 2 SS Cell polarityFKS1 CNB1 YKL190W 2 SL Cell wall organization and biogenesisFKS1 VPS67 YKR020W 0 SS Vacuolar organization and biogenesisFKS1 DBP7 YKR024C 2 SS RNA processingFKS1 SPA2 YLL021W 0 SS Cell polarityFKS1 FPS1 YLL043W 2 SS TransportFKS1 YLR021W YLR021W 2 SS UnknownFKS1 QRI5 YLR204W 2 SS UnknownFKS1 MMS22 YLR320W 0 SL UnknownFKS1 CHS5 YLR330W 3 SL Cell wall organization and biogenesisFKS1 MID2 YLR332W 0 SL Cell wall organization and biogenesisFKS1 KRE21 YLR338W 0 SL UnknownFKS1 ROM2 YLR371W 0 SL Cell wall organization and biogenesisFKS1 PSP2 YML017W 2 SS UnknownFKS1 YMR073C YMR073C 2 SS UnknownFKS1 CRZ1 YNL027W 2 SL Pol II transcriptionFKS1 YDJ1 YNL064C 0 SS Mitochondrion organization and biogenesisFKS1 RPL16B YNL069C 2 SS Protein synthesisFKS1 YNL171C YNL171C 0 SL UnknownFKS1 BNI4 YNL233W 0 SL CytokinesisFKS1 BNI1 YNL271C 0 SS SL Cell polarityFKS1 RIM21 YNL294C 2 SS UnknownFKS1 BRE5 YNR051C 2 SL UnknownFKS1 YOL003C YOL003C 0 SS UnknownFKS1 TOP1 YOL006C 2 SS Chromatin/chromosome structureFKS1 DFG16 YOR030W 0 SS DifferentiationFKS1 SHE4 YOR035C 0 SS DifferentiationFKS1 RIM20 YOR275C 0 SS Cell stressFKS1 RPL20B YOR312C 2 SS Protein synthesisFKS1 PHO85 YPL031C 2 SL Cell cycle controlFKS1 YPL041C YPL041C 0 SS UnknownFKS1 RLM1 YPL089C 3 SL Pol II transcriptionFKS1 YPL144W YPL144W 2 SS MeiosisFKS1 BEM4 YPL161C 3 SS Cell polarityFKS1 YPL261C YPL261C 2 SS UnknownFKS1 CSR2 YPR030W 2 SS Cell wall organization and biogenesisGAS1 YAL053W YAL053W 3 SL UnknownGAS1 CHS3 YBR023C 0 SS Cell wall organization and biogenesisGAS1 ROT2 YBR229C 2 SL Cell wall organization and biogenesisGAS1 IMG1 YCR046C 2 SS Energy generationGAS1 PTC1 YDL006W 2 SS Signal transductionGAS1 AAD4 YDL243C 2 SS Carbohydrate metabolism

Page 97: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

GAS1 VPS61 YDR136C 3 SS Vesicular transportGAS1 RGP1 YDR137W 3 SS Vesicular transportGAS1 NBP2 YDR162C 2 SL Cell polarityGAS1 SSD1 YDR293C 2 SS Cell cycle controlGAS1 DOT1 YDR440W 2 SS Chromatin/chromosome stuctureGAS1 GNP1 YDR508C 2 SS Amino-acid metabolismGAS1 SWI4 YER111C 0 SS Cell cycle controlGAS1 BEM2 YER155C 0 SS Cell polarityGAS1 CWH41 YGL027C 0 SL Cell wall organization and biogenesisGAS1 CUE3 YGL110C 3 SS UnknownGAS1 EMP24 YGL200C 2 SL Vesicular transportGAS1 KRE11 YGR166W 0 SL Cell wall organization and biogenesisGAS1 SMI1 YGR229C 2 SL Cell wall organization and biogenesisGAS1 NEM1 YHR004C 2 SS UnknownGAS1 SLT2 YHR030C 3 SL Cell wall organization and biogenesisGAS1 QDR2 YIL121W 3 SS TransportGAS1 BCK1 YJL095W 3 SS Cell wall organization and biogenesisGAS1 BUD19 YJL188C 2 SS Cell polarityGAS1 OPI3 YJR073C 3 SS Lipid metabolismGAS1 CNB1 YKL190W 3 SS Cell wall organization and biogenesisGAS1 SIS2 YKR072C 3 SS Cell stressGAS1 RIC1 YLR039C 2 SL Vesicular transportGAS1 VPS63 YLR261C 3 SL Vacuolar organization and biogenesisGAS1 YPT6 YLR262C 3 SL Vesicular transportGAS1 CHS5 YLR330W 3 SS Cell wall organization and biogenesisGAS1 RSC2 YLR357W 3 SS Chromatin/chromosome structureGAS1 ROM2 YLR371W 0 SL Cell wall organization and biogenesisGAS1 ECM7 YLR443W 2 SS Cell wall organization and biogenesisGAS1 NAB6 YML117W 3 SL UnknownGAS1 TGL3 YMR313C 0 SL Lipid metabolismGAS1 YMR316C-A YMR316C-A 2 SS UnknownGAS1 YMR317W YMR317W 0 SL UnknownGAS1 ADH6 YMR318C 0 SL Carbohydrate metabolismGAS1 YMR326C YMR326C 0 SL UnknownGAS1 RIM21 YNL294C 2 SS UnknownGAS1 KRE1 YNL322C 0 SS Cell wall organization and biogenesisGAS1 SLG1 YOR008C 2 SL Cell wall organization and biogenesisGAS1 HAP5 YOR358W 2 SS Pol II transcriptionGAS1 PHO85 YPL031C 3 SS Cell cycle controlGAS1 YPL041C YPL041C 3 SS UnknownGAS1 RLM1 YPL089C 3 SS Pol II transcriptionGAS1 BEM4 YPL161C 3 SS SS Cell polarityGSC2 FKS1 YLR342W 2 SL SL Cell wall organization and biogenesisHKR1 MNN10 YDR245W 2 SS SS Protein modificationHKR1 DOT1 YDR440W 2 SL Chromatin/chromosome stuctureHKR1 CDC26 YFR036W 2 SL Cell cycle controlHKR1 EMP24 YGL200C 3 SL Vesicular transportHKR1 NSR1 YGR159C 3 SS Ribosomal large subunit nucleus exportHKR1 BCK1 YJL095W 3 SS Cell wall organization and biogenesisHKR1 VPS24 YKL041W 3 SL Vesicular transportHKR1 TOM37 YMR060C 3 SL Mitochondrion organization and biogenesisHKR1 YTA12 YMR089C 2 SL Energy generationHKR1 PKR1 YMR123W 3 SS SS UnknownHKR1 YDJ1 YNL064C 3 SL Mitochondrion organization and biogenesisHKR1 YNL171C YNL171C 3 SS UnknownHKR1 IFM1 YOL023W 3 SL Energy generationHKR1 ARP8 YOR141C 3 SL Cell structureHKR1 GDH1 YOR375C 3 SS Amino-acid metabolismHKR1 BEM4 YPL161C 3 SS Cell polarityHOC1 VPS8 YAL002W 3 SS Vesicular transportHOC1 SLA1 YBL007C 3 SL Cell polarity

Page 98: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

HOC1 EDE1 YBL047C 3 SS Vesicular transportHOC1 UBC4 YBR082C 3 SS Protein degradationHOC1 RPS6B YBR181C 2 SS Protein synthesisHOC1 SAC6 YDR129C 3 SS Cell structureHOC1 RVS167 YDR388W 3 SL Cell polarityHOC1 SPF1 YEL031W 3 SL Small molecule transportHOC1 RPL1B YGL135W 3 SS SS Protein synthesisHOC1 PAC10 YGR078C 3 SS Cell structureHOC1 PEX4 YGR133W 3 SL Peroxisome organization and biogenesisHOC1 ARD1 YHR013C 3 SS Chromatin/chromosome structureHOC1 BCK1 YJL095W 3 SL Cell wall organization and biogenesisHOC1 RPA34 YJL148W 3 SS Protein synthesisHOC1 SWI3 YJL176C 2 SS Chromatin/chromosome structureHOC1 POL32 YJR043C 0 SS DNA replicationHOC1 CSN12 YJR084W 2 SL UnknownHOC1 RPS4A YJR145C 3 SS Protein synthesisHOC1 YPT52 YKR014C 3 SS Vesicular transportHOC1 VPS67 YKR020W 3 SS Vacuolar organization and biogenesisHOC1 NUP133 YKR082W 3 SS Nuclear-cytoplasmic transportHOC1 RPL22A YLR061W 3 SS Protein synthesisHOC1 CSF1 YLR087C 2 SS Cell stressHOC1 HCR1 YLR192C 3 SL Protein synthesisHOC1 ATP14 YLR295C 2 SS Energy generationHOC1 VRP1 YLR337C 3 SL Cell polarityHOC1 KRE21 YLR338W 3 SS UnknownHOC1 VPS38 YLR360W 3 SL Vesicular transportHOC1 COG8 YML071C 2 SS Vesicular transportHOC1 GIM5 YML094W 3 SS Cell structureHOC1 VPS9 YML097C 3 SS Vesicular transportHOC1 VAN1 YML115C 3 SS SS Protein modificationHOC1 TOM37 YMR060C 3 SL Mitochondrion organization and biogenesisHOC1 CIK1 YMR198W 3 SS MitosisHOC1 GIM3 YNL153C 3 SS Cell structureHOC1 KRE1 YNL322C 3 SS Cell wall organization and biogenesisHOC1 YNR005C YNR005C 3 SL SS UnknownHOC1 BRE5 YNR051C 3 SL UnknownHOC1 SHE4 YOR035C 3 SL DifferentiationHOC1 VPS21 YOR089C 3 SS SS Vesicular transportHOC1 PHO85 YPL031C 0 SL Cell cycle controlHOC1 COX10 YPL172C 3 SS Energy generationHOG1 YBL083C YBL083C 2 SS UnknownHOG1 SOY YBR194W 3 SS UnknownHOG1 SEM1 YDR363W-A 2 SS Vesicular transportHOG1 ERD1 YDR414C 2 SS Protein modificationHOG1 ITR1 YDR497C 3 SS TransportHOG1 EMP24 YGL200C 2 SS Vesicular transportHOG1 DBF2 YGR092W 3 SS Cell cycle controlHOG1 MNN11 YJL183W 2 SS Protein modificationHOG1 VPS24 YKL041W 3 SL Vesicular transportHOG1 MST1 YKL194C 2 SS Protein synthesisHOG1 YLR358C YLR358C 2 SS UnknownHOG1 SKI2 YLR398C 2 SS RNA turnoverHOG1 VPS9 YML097C 2 SL Vesicular transportHOG1 YTA12 YMR089C 2 SS Energy generationHOG1 CIK1 YMR198W 2 SS MitosisHOG1 SCS7 YMR272C 3 SL Lipid metabolismHOG1 YNL171C YNL171C 3 SS UnknownHOG1 IES2 YNL215W 3 SS SS UnknownHOG1 PDR17 YNL264C 2 SS Vesicular transportHOG1 KRE25 YNL296W 3 SS UnknownHOG1 LEO1 YOR123C 3 SS SS Chromatin/chromosome structure

Page 99: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

HOG1 BIT89 YPL180W 3 SS Lipid metabolismHOG1 YPR045C YPR045C 2 SS UnknownKNH1 VPS8 YAL002W 2 SS Vesicular transportKNH1 EDS1 YBR033W 2 SS Pol II transcriptionKNH1 RPN4 YDL020C 3 SS Protein degradationKNH1 YDL033C YDL033C 2 SS UnknownKNH1 PEX19 YDL065C 2 SL Peroxisome organization and biogenesisKNH1 PEX5 YDR244W 3 SS Lipid metabolismKNH1 YDR249C YDR249C 2 SS UnknownKNH1 PEX3 YDR329C 3 SS Peroxisome organization and biogenesisKNH1 PTP3 YER075C 3 SS Signal transductionKNH1 DST1 YGL043W 2 SS Pol II transcriptionKNH1 YGR064W YGR064W 3 SS UnknownKNH1 PEX4 YGR133W 2 SS Peroxisome organization and biogenesisKNH1 PRE9 YGR135W 3 SS Protein degradationKNH1 NSR1 YGR159C 3 SS Ribosomal large subunit nucleus exportKNH1 PSD2 YGR170W 3 SS Lipid metabolismKNH1 YGR206W YGR206W 2 SS UnknownKNH1 RPS0A YGR214W 3 SS Protein synthesisKNH1 YHL005C YHL005C 2 SS UnknownKNH1 ARD1 YHR013C 3 SL Chromatin/chromosome structureKNH1 YHR034C YHR034C 2 SS Protein synthesisKNH1 RPS4B YHR203C 2 SS Protein synthesisKNH1 QDR2 YIL121W 2 SL TransportKNH1 RPA34 YJL148W 3 SS Protein synthesisKNH1 VPS35 YJL154C 2 SS Vesicular transportKNH1 KRE9 YJL174W 0 SL Protein modificationKNH1 IXR1 YKL032C 3 SS DNA repairKNH1 YPK1 YKL126W 2 SL EndocytosisKNH1 PEX13 YLR191W 2 SS Peroxisome organization and biogenesisKNH1 YLR282C YLR282C 2 SS UnknownKNH1 CHS5 YLR330W 2 SS Cell wall organization and biogenesisKNH1 ORM2 YLR350W 3 SS Cell wall organization and biogenesisKNH1 VPS38 YLR360W 2 SS Vesicular transportKNH1 COG8 YML071C 2 SS Vesicular transportKNH1 IMP2 YMR035W 3 SS Mitochondrion organization and biogenesisKNH1 TOM37 YMR060C 3 SS SS Mitochondrion organization and biogenesisKNH1 RPS10B YMR230W 2 SS Protein synthesisKNH1 YNL171C YNL171C 2 SS UnknownKNH1 PEX6 YNL329C 3 SL Lipid metabolismKNH1 VPS5 YOR069W 3 SS Vesicular transportKNH1 GYP1 YOR070C 3 SS Vesicular transportKNH1 YPR197C YPR197C 2 SS UnknownKRE11 RRN10 YBL025W 3 SS Pol I transcriptionKRE11 ECM21 YBL101C 3 SS Cell wall organization and biogenesisKRE11 MUM2 YBR057C 3 SS MeiosisKRE11 FYV5 YCL058C 3 SS UnknownKRE11 PER1 YCR044C 3 SS SS Other metabolismKRE11 DOT1 YDR440W 3 SS Chromatin/chromosome stuctureKRE11 YEL048C YEL048C 3 SL UnknownKRE11 GUP1 YGL084C 3 SS Lipid metabolismKRE11 MMM2 YGL219C 3 SS UnknownKRE11 CHO2 YGR157W 3 SS Lipid metabolismKRE11 SMI1 YGR229C 0 SS Cell wall organization and biogenesisKRE11 ARD1 YHR013C 3 SL Chromatin/chromosome structureKRE11 SLT2 YHR030C 3 SS Cell wall organization and biogenesisKRE11 BCK1 YJL095W 3 SL Cell wall organization and biogenesisKRE11 KRE9 YJL174W 0 SL Protein modificationKRE11 SWI3 YJL176C 2 SS Chromatin/chromosome structureKRE11 ILM1 YJR118C 3 SS SS Energy generationKRE11 VPS24 YKL041W 3 SL Vesicular transport

Page 100: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

KRE11 CTK1 YKL139W 3 SS Pol II transcriptionKRE11 VPS67 YKR020W 3 SL Vacuolar organization and biogenesisKRE11 VID22 YLR373C 3 SS Vacuolar organization and biogenesisKRE11 TOM37 YMR060C 3 SS Mitochondrion organization and biogenesisKRE11 YTA12 YMR089C 3 SL Energy generationKRE11 ASC1 YMR116C 3 SS Protein synthesisKRE11 GAS1 YMR307W 3 SS Cell wall organization and biogenesisKRE11 YNL171C YNL171C 3 SL UnknownKRE11 KRE1 YNL322C 0 SL Cell wall organization and biogenesisKRE11 PEX6 YNL329C 3 SS Lipid metabolismKRE11 TRS33 YOR115C 3 SL Vesicular transportKRE11 RPL20B YOR312C 3 SS Protein synthesisKRE11 BTS1 YPL069C 3 SL Protein modificationKRE6 PEX22 YAL055W 3 SS UnknownKRE6 YBL053W YBL053W 2 SL UnknownKRE6 YBR042C YBR042C 2 SL Lipid metabolismKRE6 YDL206W YDL206W 3 SL UnknownKRE6 RGP1 YDR137W 2 SL Vesicular transportKRE6 RTN1 YDR233C 2 SL UnknownKRE6 YDR248C YDR248C 2 SL UnknownKRE6 GGA1 YDR358W 2 SL Vesicular transportKRE6 EFT2 YDR385W 2 SL Protein synthesisKRE6 YEL047C YEL047C 2 SL Other metabolismKRE6 RPO41 YFL036W 3 SS Mitochondrion organization and biogenesisKRE6 YGL081W YGL081W 2 SL UnknownKRE6 RPL1B YGL135W 2 SL Protein synthesisKRE6 YGL196W YGL196W 2 SL UnknownKRE6 EMP24 YGL200C 2 SS Vesicular transportKRE6 CLG1 YGL215W 2 SL UnknownKRE6 RTF1 YGL244W 2 SL Pol II transcriptionKRE6 VMA21 YGR105W 2 SS Vacuolar organization and biogenesisKRE6 RPL34B YIL052C 3 SS Protein synthesisKRE6 SWI3 YJL176C 2 SL Chromatin/chromosome structureKRE6 VPS24 YKL041W 2 SS Vesicular transportKRE6 OAC1 YKL120W 2 SS TransportKRE6 FPS1 YLL043W 2 SS TransportKRE6 POM34 YLR018C 2 SL Nuclear-cytoplasmic transportKRE6 ACE2 YLR131C 2 SS Pol II TranscriptionKRE6 PUS5 YLR165C 2 SL Other metabolismKRE6 VAN1 YML115C 2 SL Protein modificationKRE6 VAM10 YOR068C 2 SS Vacuolar organization and biogenesisKRE6 DIA2 YOR080W 2 SS DifferentiationKRE6 PRM3 YPL192C 2 SL Mating responseKRE9 KNH1 YDL049C 0 SL Cell wall organization and biogenesisKRE9 KRE11 YGR166W 0 SL Cell wall organization and biogenesisKRE9 QCR8 YJL166W 3 SL SL Energy generationKRE9 YJR011C YJR011C 2 SL SL UnknownKRE9 BAT2 YJR148W 2 SL SL Amino-acid metabolismKRE9 YKL177W YKL177W 3 SL SL UnknownKRE9 STM1 YLR150W 2 SL SL Nucleotide metabolismKRE9 MRE11 YMR224C 3 SL SL DNA repairKRE9 ARK1 YNL020C 2 SL SL Cell polarityKRE9 KRE1 YNL322C 0 SL Cell wall organization and biogenesisKRE9 PRM3 YPL192C 2 SL SL Mating responseKTR3 KRE21 YLR338W 3 SL SS UnknownKTR3 TOM37 YMR060C 3 SS SS Mitochondrion organization and biogenesisLAS21 FUI1 YBL042C 3 SS Small molecule transportLAS21 ECM21 YBL101C 2 SS Cell wall organization and biogenesisLAS21 YBL104C YBL104C 3 SS UnknownLAS21 ECM8 YBR076W 3 SS Cell wall organization and biogenesisLAS21 AGP1 YCL025C 2 SS Transport

Page 101: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

LAS21 PEX19 YDL065C 3 SL Peroxisome organization and biogenesisLAS21 YDL096C YDL096C 2 SS UnknownLAS21 SEM1 YDR363W-A 2 SL Vesicular transportLAS21 RPL9A YGL147C 3 SS Protein synthesisLAS21 ARD1 YHR013C 3 SS Chromatin/chromosome structureLAS21 IMP2' YIL154C 2 SL Carbohydrate metabolismLAS21 BCK1 YJL095W 3 SS Cell wall organization and biogenesisLAS21 CHS6 YJL099W 2 SS Cell wall organization and biogenesisLAS21 RPA34 YJL148W 3 SS Protein synthesisLAS21 CSF1 YLR087C 3 SS Cell stressLAS21 PEX15 YOL044W 3 SS Cell structureLAS21 RPL21B YPL079W 2 SS Protein synthesisLAS21 YPL080C YPL080C 2 SS UnknownLAS21 LEA1 YPL213W 3 SS RNA splicingLAS21 YPR045C YPR045C 3 SS UnknownLRE1 IMP2 YMR035W 3 SS Mitochondrion organization and biogenesisMID2 SAC6 YDR129C 3 SS SS Cell structureMID2 SMI1 YGR229C 3 SS SS Cell wall organization and biogenesisMID2 ILM1 YJR118C 3 SL SL Energy generationMID2 FPS1 YLL043W 3 SS SL TransportMID2 CCW12 YLR110C 2 SS SL Cell wall organization and biogenesisMID2 YLR111W YLR111W 2 SL SL UnknownMID2 KRE21 YLR338W 3 SL SL UnknownMID2 ROM2 YLR371W 3 SL SL Cell wall organization and biogenesisMID2 VAN1 YML115C 3 SS SL Protein modificationMID2 SLG1 YOR008C 3 SL SL Cell wall organization and biogenesisMNL1 RPL20B YOR312C 2 SS SS Protein synthesisMNS1 CKB1 YGL019W 0 SS Cell cycle controlSKN1 RRN10 YBL025W 3 SL Pol I transcriptionSKN1 PEX5 YDR244W 2 SL Lipid metabolismSKN1 PEX4 YGR133W 3 SL Peroxisome organization and biogenesisSKN1 PRE9 YGR135W 3 SL Protein degradationSKN1 LST4 YKL176C 2 SS Vesicular transportSKN1 IFM1 YOL023W 3 SL Energy generationSKT5 SLA1 YBL007C 3 SS Cell polaritySKT5 EDE1 YBL047C 3 SS Vesicular transportSKT5 UBP13 YBL067C 2 SS Protein modificationSKT5 AST1 YBL069W 2 SS Protein targetingSKT5 RPS8A YBL072C 3 SS Protein synthesisSKT5 SAC6 YDR129C 3 SL Cell structureSKT5 UME6 YDR207C 0 SS MeiosisSKT5 MNN10 YDR245W 3 SL Protein modificationSKT5 ATP17 YDR377W 3 SS Energy generationSKT5 RVS167 YDR388W 0 SL Cell polaritySKT5 SPF1 YEL031W 3 SS Small molecule transportSKT5 SWI4 YER111C 0 SS Cell cycle controlSKT5 RPO41 YFL036W 0 SS Mitochondrion organization and biogenesisSKT5 FAB1 YFR019W 0 SS Lipid metabolismSKT5 GUP1 YGL084C 0 SL Lipid metabolismSKT5 SMI1 YGR229C 0 SL Cell wall organization and biogenesisSKT5 SLT2 YHR030C 3 SS Cell wall organization and biogenesisSKT5 BCK1 YJL095W 3 SL Cell wall organization and biogenesisSKT5 RPA34 YJL148W 0 SS Protein synthesisSKT5 OPI3 YJR073C 3 SS Lipid metabolismSKT5 ILM1 YJR118C 3 SL Energy generationSKT5 SMY1 YKL079W 3 SS Cell polaritySKT5 YPK1 YKL126W 3 SS EndocytosisSKT5 LST4 YKL176C 3 SS Vesicular transportSKT5 FPS1 YLL043W 3 SS TransportSKT5 CSF1 YLR087C 3 SS Cell stressSKT5 CCW12 YLR110C 0 SS Cell wall organization and biogenesis

Page 102: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

SKT5 YLR111W YLR111W 0 SS UnknownSKT5 SEC22 YLR268W 2 SS Vesicular transportSKT5 VRP1 YLR337C 3 SL Cell polaritySKT5 KRE21 YLR338W 3 SL UnknownSKT5 FKS1 YLR342W 0 SL Cell wall organization and biogenesisSKT5 ARC18 YLR370C 2 SS Cell polaritySKT5 TUS1 YLR425W 0 SS UnknownSKT5 VAN1 YML115C 3 SL Protein modificationSKT5 YTA12 YMR089C 3 SS Energy generationSKT5 TPM1 YNL079C 3 SL Cell structureSKT5 BNI1 YNL271C 0 SS Cell polaritySKT5 CLA4 YNL298W 3 SS Cell polaritySKT5 BRE5 YNR051C 3 SS UnknownSKT5 SHE4 YOR035C 3 SS DifferentiationSKT5 RSA1 YPL193W 2 SS Ribosomal large subunit assembly and maintenanceSMI1 SLA1 YBL007C 3 SL Cell polaritySMI1 SKT5 YBL061C 2 SS Cell wall organization and biogenesisSMI1 ECM21 YBL101C 3 SS Cell wall organization and biogenesisSMI1 CHS3 YBR023C 3 SL Cell wall organization and biogenesisSMI1 FAT1 YBR041W 2 SL Lipid metabolismSMI1 UBC4 YBR082C 3 SL Protein degradationSMI1 CCZ1 YBR131W 2 SL Vesicular transportSMI1 TYR1 YBR166C 2 SL Amino-acid metabolismSMI1 BEM1 YBR200W 3 SL Cell polaritySMI1 PTC1 YDL006W 3 SL Signal transductionSMI1 RPA14 YDR156W 2 SL Pol I transcriptionSMI1 NBP2 YDR162C 3 SL Cell polaritySMI1 MNN10 YDR245W 3 SL Protein modificationSMI1 SBE2 YDR351W 3 SS Cell wall organization and biogenesisSMI1 RVS167 YDR388W 2 SS Cell polaritySMI1 SPF1 YEL031W 2 SL Small molecule transportSMI1 SWI4 YER111C 3 SS Cell cycle controlSMI1 UBP3 YER151C 3 SS Protein modificationSMI1 BEM2 YER155C 3 SL Cell polaritySMI1 PDA1 YER178W 2 SS Mitochondrion organization and biogenesisSMI1 RPL29 YFR032C-A 2 SS Protein synthesisSMI1 RIM8 YGL046W 2 SS UnknownSMI1 DOC1 YGL240W 3 SS Cell cycle controlSMI1 PRE9 YGR135W 3 SS Protein degradationSMI1 KRE11 YGR166W 2 SS Cell wall organization and biogenesisSMI1 RPS0A YGR214W 2 SS Protein synthesisSMI1 CCH1 YGR217W 2 SL TransportSMI1 YGR237C YGR237C 2 SL UnknownSMI1 SLT2 YHR030C 2 SL Cell wall organization and biogenesisSMI1 ARP1 YHR129C 0 SS MitosisSMI1 CHS7 YHR142W 2 SL Cell wall organization and biogenesisSMI1 CTF8 YHR191C 2 SS Chromatin/chromosome structureSMI1 RPN10 YHR200W 2 SS Pol II transcriptionSMI1 BCK1 YJL095W 3 SL Cell wall organization and biogenesisSMI1 CHS6 YJL099W 3 SL Cell wall organization and biogenesisSMI1 PHO86 YJL117W 2 SS Phosphate metabolismSMI1 MNN11 YJL183W 3 SS Protein modificationSMI1 BUD19 YJL188C 3 SS Cell polaritySMI1 ILM1 YJR118C 3 SL Energy generationSMI1 ELM1 YKL048C 3 SS Cell polaritySMI1 CNB1 YKL190W 2 SS Cell wall organization and biogenesisSMI1 VPS67 YKR020W 2 SS Vacuolar organization and biogenesisSMI1 SPA2 YLL021W 2 SS Cell polaritySMI1 FPS1 YLL043W 3 SL TransportSMI1 RIC1 YLR039C 3 SS Vesicular transportSMI1 YPT6 YLR262C 2 SS Vesicular transport

Page 103: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

SMI1 MMS22 YLR320W 3 SS UnknownSMI1 CHS5 YLR330W 3 SL SL Cell wall organization and biogenesisSMI1 MID2 YLR332W 3 SS Cell wall organization and biogenesisSMI1 YLR358C YLR358C 3 SS UnknownSMI1 ROM2 YLR371W 3 SS Cell wall organization and biogenesisSMI1 IKI3 YLR384C 2 SS Pol II transcriptionSMI1 VAN1 YML115C 3 SL Protein modificationSMI1 NAB6 YML117W 2 SS UnknownSMI1 LYS7 YMR038C 3 SL Amino-acid metabolismSMI1 ASC1 YMR116C 3 SS Protein synthesisSMI1 PFK2 YMR205C 2 SS Carbohydrate metabolismSMI1 GAS1 YMR307W 3 SS Cell wall organization and biogenesisSMI1 YNL171C YNL171C 3 SL UnknownSMI1 BNI4 YNL233W 3 SL CytokinesisSMI1 BNI1 YNL271C 2 SS Cell polaritySMI1 CLA4 YNL298W 3 SS Cell polaritySMI1 KRE1 YNL322C 3 SS Cell wall organization and biogenesisSMI1 BRE5 YNR051C 3 SL UnknownSMI1 YOL003C YOL003C 3 SS UnknownSMI1 DFG16 YOR030W 2 SS DifferentiationSMI1 RIM20 YOR275C 3 SS Cell stressSMI1 PHO85 YPL031C 3 SS Cell cycle controlSMI1 YPL077C YPL077C 2 SL UnknownSMI1 RLM1 YPL089C 3 SL Pol II transcriptionSMI1 CTF4 YPR135W 3 SS Chromatin/chromosome structureSVP26 BUD25 YER014C-A 3 SS Cell polaritySVP26 EMP24 YGL200C 3 SS Vesicular transportSVP26 MST1 YKL194C 3 SS Protein synthesisSVP26 VPS38 YLR360W 2 SS Vesicular transportSVP26 BDF1 YLR399C 3 SS Pol II TranscriptionSVP26 AEP2 YMR282C 3 SL Mitochondrion organization and biogenesisSVP26 YDJ1 YNL064C 3 SS Mitochondrion organization and biogenesisSVP26 HTZ1 YOL012C 2 SS Chromatin/chromosome structureYKL037W PTC1 YDL006W 3 SS Signal transductionYKL037W UBP3 YER151C 2 SS Protein modificationYKL037W SLT2 YHR030C 2 SL Cell wall organization and biogenesisYKL037W BCK1 YJL095W 3 SL Cell wall organization and biogenesisYKL037W FPS1 YLL043W 2 SS TransportYKL037W ABF2 YMR072W 3 SS Mitochondrion organization and biogenesisYLR057W EMP24 YGL200C 2 SS Vesicular transportYLR057W PEX6 YNL329C 2 SS Lipid metabolismYUR1 SLT2 YHR030C 2 SL Cell wall organization and biogenesisYUR1 BCK1 YJL095W 3 SL Cell wall organization and biogenesisYUR1 UBI4 YLL039C 0 SS Protein degradationYUR1 PEX15 YOL044W 2 SS Cell structureRVS161 DEP1 YAL013W 3 SS Lipid metabolismRVS161 SLA1 YBL007C 3 SS Cell polarityRVS161 SKT5 YBL061C 1 SS Cell wall organization and biogenesisRVS161 MNN2 YBR015C 3 SS Protein modificationRVS161 CHS3 YBR023C 1 SS Cell wall organization and biogenesisRVS161 RXT2 YBR095C 3 SS UnknownRVS161 TPS1 YBR126C 3 SS Carbohydrate metabolismRVS161 YBR255W YBR255W 3 SS UnknownRVS161 CYK3 YDL117W 3 SS CytokinesisRVS161 MNN10 YDR245W 3 SL Protein modificationRVS161 SUM1 YDR310C 3 SS Chromatin/chromosome structureRVS161 GIM4 YEL003W 1 SS Cell structureRVS161 SPF1 YEL031W 3 SL Small molecule transportRVS161 SWI4 YER111C 3 SL Cell cycle controlRVS161 GUP1 YGL084C 3 SL Lipid metabolismRVS161 PAC10 YGR078C 3 SL Cell structure

Page 104: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

RVS161 SLT2 YHR030C 3 SL Cell wall organization and biogenesisRVS161 CHS7 YHR142W 1 SS Cell wall organization and biogenesisRVS161 CAP2 YIL034C 3 SL Cell structureRVS161 SDS3 YIL084C 3 SL Chromatin/chromosome structureRVS161 YIB3 YIR003W 3 SS UnknownRVS161 BBC1 YJL020C 3 SS Cell polarityRVS161 BCK1 YJL095W 3 SL Cell wall organization and biogenesisRVS161 CHS6 YJL099W 1 SS Cell wall organization and biogenesisRVS161 HOC1 YJR075W 3 SS Cell wall organization and biogenesisRVS161 CAP1 YKL007W 3 SL Cell structureRVS161 EAP1 YKL204W 3 SL Protein synthesisRVS161 DOA1 YKL213C 3 SS Protein degradationRVS161 CSF1 YLR087C 3 SL Cell stressRVS161 CCW12 YLR110C 3 SL Cell wall organization and biogenesisRVS161 YLR111W YLR111W 3 SS UnknownRVS161 YKE2 YLR200W 3 SS Cell structureRVS161 SEC22 YLR268W 3 SS Vesicular transportRVS161 CHS5 YLR330W 3 SS Cell wall organization and biogenesisRVS161 GIM5 YML094W 1 SL Cell structureRVS161 MYO5 YMR109W 3 SS Cell polarityRVS161 SAP30 YMR263W 3 SS Chromatin/chromosome structureRVS161 END3 YNL084C 1 SS EndocytosisRVS161 PHO23 YNL097C 3 SS Phosphate metabolismRVS161 GIM3 YNL153C 3 SS Cell structureRVS161 BNI4 YNL233W 1 SS CytokinesisRVS161 CLA4 YNL298W 1 SS Cell polarityRVS161 KRE1 YNL322C 3 SS Cell wall organization and biogenesisRVS161 SIN3 YOL004W 3 SS Pol II transcriptionRVS161 VPS21 YOR089C 3 SS Vesicular transportRVS161 RUD3 YOR216C 3 SS Vesicular transportRVS161 MNN9 YPL050C 1 SL Protein modificationRVS167 DEP1 YAL013W 3 SS Lipid metabolismRVS167 SLA1 YBL007C 3 SS Cell polarityRVS167 SKT5 YBL061C 1 SS Cell wall organization and biogenesisRVS167 MNN2 YBR015C 3 SS Protein modificationRVS167 CHS3 YBR023C 1 SS Cell wall organization and biogenesisRVS167 RXT2 YBR095C 3 SS UnknownRVS167 TPS1 YBR126C 3 SS Carbohydrate metabolismRVS167 YBR255W YBR255W 3 SS UnknownRVS167 CYK3 YDL117W 3 SS CytokinesisRVS167 MNN10 YDR245W 3 SL Protein modificationRVS167 SUM1 YDR310C 3 SS Chromatin/chromosome structureRVS167 GIM4 YEL003W 1 SS Cell structureRVS167 SPF1 YEL031W 3 SL Small molecule transportRVS167 SWI4 YER111C 3 SL Cell cycle controlRVS167 GUP1 YGL084C 3 SS Lipid metabolismRVS167 PAC10 YGR078C 3 SL Cell structureRVS167 SLT2 YHR030C 3 SL Cell wall organization and biogenesisRVS167 CHS7 YHR142W 1 SS Cell wall organization and biogenesisRVS167 CAP2 YIL034C 3 SL Cell structureRVS167 SDS3 YIL084C 3 SL Chromatin/chromosome structureRVS167 YIB3 YIR003W 3 SS UnknownRVS167 BBC1 YJL020C 3 SS Cell polarityRVS167 BCK1 YJL095W 3 SL Cell wall organization and biogenesisRVS167 CHS6 YJL099W 1 SS Cell wall organization and biogenesisRVS167 HOC1 YJR075W 3 SS Cell wall organization and biogenesisRVS167 CAP1 YKL007W 3 SL Cell structureRVS167 EAP1 YKL204W 3 SS Protein synthesisRVS167 DOA1 YKL213C 3 SS Protein degradationRVS167 CSF1 YLR087C 3 SL Cell stressRVS167 CCW12 YLR110C 3 SL Cell wall organization and biogenesis

Page 105: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

RVS167 YLR111W YLR111W 3 SS UnknownRVS167 YKE2 YLR200W 3 SS Cell structureRVS167 SEC22 YLR268W 3 SS Vesicular transportRVS167 CHS5 YLR330W 3 SS Cell wall organization and biogenesisRVS167 GIM5 YML094W 1 SL Cell structureRVS167 MYO5 YMR109W 3 SS Cell polarityRVS167 SAP30 YMR263W 3 SS Chromatin/chromosome structureRVS167 END3 YNL084C 1 SS EndocytosisRVS167 PHO23 YNL097C 3 SS Phosphate metabolismRVS167 GIM3 YNL153C 3 SS Cell structureRVS167 BNI4 YNL233W 1 SS CytokinesisRVS167 CLA4 YNL298W 1 SS Cell polarityRVS167 KRE1 YNL322C 3 SS Cell wall organization and biogenesisRVS167 SIN3 YOL004W 3 SS Pol II transcriptionRVS167 VPS21 YOR089C 3 SS Vesicular transportRVS167 RUD3 YOR216C 3 SS Vesicular transportRVS167 MNN9 YPL050C 1 SL Protein modificationARL1 PER1 YCR044C 0 SS Other metabolismARL1 VAM6 YDL077C 0 SS Vesicular transportARL1 ARR4 YDL100C 0 SS Small molecule transportARL1 ARF1 YDL192W 0 SL TransportARL1 GSS1 YDR108W 3 SL Vesicular transportARL1 VPS61 YDR136C 3 SL Vesicular transportARL1 RGP1 YDR137W 3 SL Vesicular transportARL1 NBP2 YDR162C 3 SL SL Cell polarityARL1 RAV2 YDR202C 0 SS Small molecule transportARL1 YDR203W YDR203W 0 SS UnknownARL1 RMD7 YER083C 0 SL Cell wall organization and biogenesisARL1 GLO3 YER122C 0 SL Vesicular transportARL1 COG7 YGL005C 1 SL Vesicular transportARL1 VMA21 YGR105W 0 SS Vacuolar organization and biogenesisARL1 GOS1 YHL031C 3 SS Vesicular transportARL1 VPS29 YHR012W 0 SS Vesicular transportARL1 VPS35 YJL154C 0 SS Vesicular transportARL1 CPR7 YJR032W 3 SL Protein foldingARL1 RAV1 YJR033C 1 SS Vacuolar organization and biogenesisARL1 YKL118W YKL118W 0 SS UnknownARL1 VPH2 YKL119C 0 SL Vacuolar organization and biogenesisARL1 VPS1 YKR001C 2 SL Vesicular transportARL1 VPS67 YKR020W 3 SL Vacuolar organization and biogenesisARL1 RIC1 YLR039C 3 SL Vesicular transportARL1 ARV1 YLR242C 0 SS Lipid metabolismARL1 VPS63 YLR261C 3 SL Vacuolar organization and biogenesisARL1 YPT6 YLR262C 3 SL Vesicular transportARL1 VMA6 YLR447C 0 SS Vacuolar organization and biogenesisARL1 COG8 YML071C 3 SL Vesicular transportARL1 MVP1 YMR004W 0 SS Vesicular transportARL1 STV1 YMR054W 0 SS Vacuolar organization and biogenesisARL1 PKR1 YMR123W 1 SS UnknownARL1 COG6 YNL041C 3 SL Vesicular transportARL1 YNL043C YNL043C 0 SS UnknownARL1 YIP3 YNL044W 0 SS Vesicular transportARL1 COG5 YNL051W 3 SL Vesicular transportARL1 KEX2 YNL238W 0 SS Protein modificationARL1 KRE25 YNL296W 2 SS UnknownARL1 MON2 YNL297C 2 SL Vacuolar organization and biogenesisARL1 TLG2 YOL018C 1 SS Vesicular transportARL1 VAM10 YOR068C 0 SS Vacuolar organization and biogenesisARL1 VPS5 YOR069W 1 SS Vesicular transportARL1 GYP1 YOR070C 2 SL Vesicular transportARL1 VPS17 YOR132W 0 SS Vesicular transport

Page 106: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

HPR5 MMS4 YBR098W 2 SS DNA repairHPR5 YBR099C YBR099C 0 SS UnknownHPR5 DCC1 YCL016C 0 SS Chromatin/chromosome structureHPR5 MRC1 YCL060C 3 SL DNA repairHPR5 ESC2 YDR363W 3 SS Chromatin/chromosome structureHPR5 XRS2 YDR369C 1 SS DNA repairHPR5 MUS81 YDR386W 0 SS DNA repairHPR5 RAD54 YGL163C 1 SL DNA repairHPR5 RRM3 YHR031C 3 SS DNA replicationHPR5 RTT107 YHR154W 3 SS Chromatin/chromosome structureHPR5 CTF8 YHR191C 0 SS Chromatin/chromosome structureHPR5 MPH1 YIR002C 3 SS DNA repairHPR5 POL32 YJR043C 3 SS DNA replicationHPR5 RAD27 YKL113C 3 SS DNA repairHPR5 TOP3 YLR234W 1 SS Chromatin/chromosome structureHPR5 YLR235C YLR235C 1 SS UnknownHPR5 MMS22 YLR320W 1 SS UnknownHPR5 CSM3 YMR048W 3 SS MeiosisHPR5 CTF18 YMR078C 0 SL SL Chromatin/chromosome structureHPR5 SGS1 YMR190C 2 SS DNA repairHPR5 RAD50 YNL250W 1 SS DNA repairHPR5 TOF1 YNL273W 0 SS DNA repairHPR5 ELG1 YOR144C 0 SS DNA repairHPR5 CHL1 YPL008W 2 SS Chromatin/chromosome structureHPR5 NCE4 YPL024W 0 SL Cell wall organization and biogenesisHPR5 CTF4 YPR135W 2 SS Chromatin/chromosome structureHPR5 MMS1 YPR164W 2 SS DNA repairRRM3 DCC1 YCL016C 1 SS Chromatin/chromosome structureRRM3 MRC1 YCL061C 3 SL DNA repairRRM3 PPH3 YDR075W 3 SL Cell structureRRM3 ESC2 YDR363W 2 SL Chromatin/chromosome structureRRM3 PMR1 YGL167C 3 SL Small molecule transportRRM3 HUR1 YGL168W 2 SL UnknownRRM3 SAE2 YGL175C 2 SS DNA repairRRM3 SOD2 YHR008C 0 SL Cell stressRRM3 RTT107 YHR154W 0 SL Chromatin/chromosome structureRRM3 CTF8 YHR191C 0 SS Chromatin/chromosome structureRRM3 RTT101 YJL047C 3 SL Protein modificationRRM3 HPR5 YJL092W 2 SL DNA repairRRM3 TOP3 YLR234W 1 SL Chromatin/chromosome structureRRM3 RAD52 YML032C 0 SS DNA repairRRM3 SGS1 YMR190C 0 SL DNA repairRRM3 MRE11 YMR224C 1 SL DNA repairRRM3 RAD50 YNL250W 1 SL DNA repairRRM3 NCE4 YPL024W 0 SL Cell wall organization and biogenesisRRM3 CTF4 YPR135W 1 SL Chromatin/chromosome structureRRM3 MMS1 YPR164W 2 SL DNA repairKRE1 DRS2 YAL026C 3 SS Vesicular transportKRE1 YAL053W YAL053W 3 SL UnknownKRE1 KRE20 YAL056C-A 2 SL UnknownKRE1 CNE1 YAL058W 2 SS Cell wall organization and biogenesisKRE1 BUD14 YAR014C 1 SS Cell polarityKRE1 SKT5 YBL061C 1 SS Cell wall organization and biogenesisKRE1 RHK1 YBL082C 3 SS Cell wall organization and biogenesisKRE1 YBL083C YBL083C 3 SS UnknownKRE1 CHS3 YBR023C 1 SS Cell wall organization and biogenesisKRE1 ROT2 YBR229C 3 SL Cell wall organization and biogenesisKRE1 PER1 YCR044C 3 SS SS Other metabolismKRE1 PTC1 YDL006W 3 SS SS Signal transductionKRE1 SAC6 YDR129C 3 SS Cell structureKRE1 NBP2 YDR162C 2 SS Cell polarity

Page 107: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

KRE1 SAC7 YDR389W 3 SL Cell structureKRE1 ERD1 YDR414C 3 SS Protein modificationKRE1 ERG28 YER044C 1 SL Lipid metabolismKRE1 BEM2 YER155C 1 SS Cell polarityKRE1 FAB1 YFR019W 2 SS SS Lipid metabolismKRE1 CWH41 YGL027C 3 SL SL Cell wall organization and biogenesisKRE1 GUP1 YGL084C 3 SL Lipid metabolismKRE1 HUR1 YGL168W 3 SS SS UnknownKRE1 KEX1 YGL203C 3 SS Protein modificationKRE1 KRE11 YGR166W 3 SS Cell wall organization and biogenesisKRE1 SMI1 YGR229C 3 SS SS Cell wall organization and biogenesisKRE1 SLT2 YHR030C 3 SS Cell wall organization and biogenesisKRE1 YUR1 YJL139C 1 SS Cell wall organization and biogenesisKRE1 KRE9 YJL174W 1 SL Protein modificationKRE1 MNN11 YJL183W 3 SL Protein modificationKRE1 OPI3 YJR073C 3 SS Lipid metabolismKRE1 HOC1 YJR075W 3 SS Cell wall organization and biogenesisKRE1 STE24 YJR117W 0 SS Protein modificationKRE1 ILM1 YJR118C 3 SS Energy generationKRE1 CNB1 YKL190W 3 SS Cell wall organization and biogenesisKRE1 VPS67 YKR020W 3 SS Vacuolar organization and biogenesisKRE1 CHS5 YLR330W 2 SS Cell wall organization and biogenesisKRE1 TOM37 YMR060C 3 SS Mitochondrion organization and biogenesisKRE1 DFG5 YMR238W 3 SS SS DifferentiationKRE1 GAS1 YMR307W 3 SS SL Cell wall organization and biogenesisKRE1 KEX2 YNL238W 3 SL Protein modificationKRE1 SHE4 YOR035C 3 SS SS DifferentiationKRE1 VPS28 YPL065W 3 SS Vesicular transportCIN1 DCC1 YCL016C 0 SL Chromatin/chromosome structureCIN1 BIK1 YCL029C 1 SL MitosisCIN1 NUM1 YDR150W 0 SL MitosisCIN1 CHL4 YDR254W 0 SS Chromatin/chromosome structureCIN1 MCM21 YDR318W 0 SS Chromatin/chromosome structureCIN1 DYN2 YDR424C 0 SS MitosisCIN1 PAC11 YDR488C 0 SL MitosisCIN1 GIM4 YEL003W 1 SL Cell structureCIN1 CIN8 YEL061C 0 SL MitosisCIN1 BIM1 YER016W 0 SL SL MitosisCIN1 MAD1 YGL086W 3 SL SL MitosisCIN1 PAC10 YGR078C 0 SL Cell structureCIN1 BUB1 YGR188C 0 SL MitosisCIN1 ARP1 YHR129C 0 SS SS MitosisCIN1 CTF8 YHR191C 0 SL Chromatin/chromosome structureCIN1 MAD3 YJL013C 0 SS MitosisCIN1 MAD2 YJL030W 1 SL MitosisCIN1 DYN1 YKR054C 0 SS SS MitosisCIN1 ARP6 YLR085C 1 SL Cell structureCIN1 GIM5 YML094W 0 SL Cell structureCIN1 TUB3 YML124C 2 SL Cell structureCIN1 CTF18 YMR078C 0 SL Chromatin/chromosome structureCIN1 JNM1 YMR294W 0 SL MitosisCIN1 GIM3 YNL153C 2 SL Cell structureCIN1 HTZ1 YOL012C 0 SS Chromatin/chromosome structureCIN1 RBL2 YOR265W 1 SL SL Cell structureCIN1 CTF19 YPL018W 0 SS Chromatin/chromosome structureCIN1 KIP2 YPL155C 0 SS MitosisCIN1 NIP100 YPL174C 0 SL MitosisCIN1 KAR9 YPL269W 0 SL MitosisCIN1 CTF4 YPR135W 0 SS Chromatin/chromosome structureROT2 PDB1 YBR221C 3 SS Carbohydrate metabolismROT2 RPO41 YFL036W 3 SS Mitochondrion organization and biogenesis

Page 108: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

ROT2 GUP1 YGL084C 3 SS Lipid metabolismROT2 CHO2 YGR157W 2 SS Lipid metabolismROT2 SLT2 YHR030C 3 SS Cell wall organization and biogenesisROT2 GGA2 YHR108W 2 SS Vesicular transportROT2 BCK1 YJL095W 3 SS Cell wall organization and biogenesisROT2 CSF1 YLR087C 3 SS Cell stressROT2 GAS1 YMR307W 3 SS Cell wall organization and biogenesisROT2 KRE1 YNL322C 3 SS Cell wall organization and biogenesisROT2 VAM10 YOR068C 2 SS Vacuolar organization and biogenesisROT2 VPS5 YOR069W 2 SS Vesicular transportROT2 GYP1 YOR070C 2 SS Vesicular transportCWH41 YBR235W YBR235W 0 SS Small molecule transportCWH41 PER1 YCR044C 2 SS Other metabolismCWH41 PTC1 YDL006W 2 SS Signal transductionCWH41 SWF3 YGL020C 3 SS UnknownCWH41 GUP1 YGL084C 3 SS Lipid metabolismCWH41 SNF4 YGL115W 3 SS Protein modificationCWH41 EMP24 YGL200C 3 SS Vesicular transportCWH41 SLT2 YHR030C 3 SL Cell wall organization and biogenesisCWH41 BCK1 YJL095W 3 SL Cell wall organization and biogenesisCWH41 CSF1 YLR087C 3 SS Cell stressCWH41 SCJ1 YMR214W 0 SS Protein foldingCWH41 GAS1 YMR307W 3 SL Cell wall organization and biogenesisCWH41 KRE1 YNL322C 0 SL SL Cell wall organization and biogenesisCWH41 LEA1 YPL213W 3 SS RNA splicingALG8 PER1 YCR044C 3 SS Other metabolismALG8 TPS2 YDR074W 3 SS Carbohydrate metabolismALG8 RPO41 YFL036W 3 SL Mitochondrion organization and biogenesisALG8 OST5 YGL226C-A 3 SL Protein modificationALG8 SLT2 YHR030C 3 SS Cell wall organization and biogenesisALG8 BCK1 YJL095W 3 SS Cell wall organization and biogenesisALG8 CSF1 YLR087C 0 SS Cell stressALG8 YLR358C YLR358C 3 SS UnknownALG8 SHE4 YOR035C 3 SS DifferentiationALG8 DIA2 YOR080W 3 SS DifferentiationALG8 OST3 YOR085W 2 SL Protein modificationDEP1 HIR1 YBL008W 0 SS Chromatin/chromosome structureDEP1 RPL19B YBL027W 0 SS Protein synthesisDEP1 SIF2 YBR103W 2 SL Chromatin/chromosome structureDEP1 SEC66 YBR171W 2 SS Vesicular transportDEP1 SNT1 YCR033W 2 SL Chromatin/chromosome structureDEP1 NHP10 YDL002C 1 SS SS UnknownDEP1 BRE1 YDL074C 1 SS SS Chromatin/chromosome stuctureDEP1 THI3 YDL080C 0 SL Amino-acid metabolismDEP1 SWI5 YDR146C 1 SS SS Pol II transcriptionDEP1 SAS4 YDR181C 1 SS SS Chromatin/chromosome structureDEP1 SWR1 YDR334W 2 SL UnknownDEP1 SEM1 YDR363W-A 0 SS Vesicular transportDEP1 SPT3 YDR392W 1 SL Chromatin/chromosome stuctureDEP1 VPS72 YDR485C 3 SL Vesicular transportDEP1 BIM1 YER016W 1 SL MitosisDEP1 SWI4 YER111C 3 SS Cell cycle controlDEP1 YER139C YER139C 0 SL UnknownDEP1 UBP6 YFR010W 0 SS Protein modificationDEP1 SOH1 YGL127C 0 SL SL DNA repairDEP1 ITC1 YGL133W 0 SS Chromatin/chromosome structureDEP1 YGL149W YGL149W 1 SS SL UnknownDEP1 YIP5 YGL161C 1 SS SS Vesicular transportDEP1 PMR1 YGL167C 0 SS Small molecule transportDEP1 HOS2 YGL194C 3 SL Chromatin/chromosome structureDEP1 RTF1 YGL244W 1 SS Pol II transcription

Page 109: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

DEP1 VMA21 YGR105W 1 SL Vacuolar organization and biogenesisDEP1 TIM13 YGR181W 3 SL Protein translocationDEP1 YGR182C YGR182C 3 SL UnknownDEP1 ELP2 YGR200C 0 SL Pol II transcriptionDEP1 YTA7 YGR270W 0 SS Vacuolar organization and biogenesisDEP1 SRB2 YHR041C 0 SL Pol II TranscriptionDEP1 VMA22 YHR060W 1 SL Vacuolar organization and biogenesisDEP1 STB5 YHR178W 0 SL Pol II transcriptionDEP1 RPN10 YHR200W 0 SL Pol II transcriptionDEP1 ASF1 YJL115W 1 SS Chromatin/chromosome structureDEP1 OPI3 YJR073C 0 SS Lipid metabolismDEP1 HIR3 YJR140C 1 SS Pol II transcriptionDEP1 YKL118W YKL118W 1 SL UnknownDEP1 SET3 YKR029C 0 SS Chromatin/chromosome structureDEP1 SPT8 YLR055C 1 SS Chromatin/chromosome structureDEP1 ARP6 YLR085C 2 SL Cell structureDEP1 CSF1 YLR087C 0 SL Cell stressDEP1 YLR111W YLR111W 0 SS UnknownDEP1 SEC22 YLR268W 0 SS Vesicular transportDEP1 IKI3 YLR384C 0 SL Pol II transcriptionDEP1 CDC73 YLR418C 0 SL Pol II transcriptionDEP1 VPS71 YML041C 3 SL Vesicular transportDEP1 PRM6 YML047C 3 SL UnknownDEP1 TOM37 YMR060C 1 SL Mitochondrion organization and biogenesisDEP1 ELP6 YMR312W 1 SL Pol II transcriptionDEP1 YNL140C YNL140C 1 SS SS UnknownDEP1 IES2 YNL215W 2 SL UnknownDEP1 CLA4 YNL298W 3 SL Cell polarityDEP1 HTZ1 YOL012C 1 SL Chromatin/chromosome structureDEP1 VPS21 YOR089C 0 SS Vesicular transportDEP1 LEO1 YOR123C 1 SS Chromatin/chromosome structureDEP1 SAS5 YOR213C 0 SS SS Chromatin/chromosome structureDEP1 ISW2 YOR304W 0 SS Chromatin/chromosome strucutreDEP1 LGE1 YPL055C 0 SS Cell cycle controlDEP1 ELP3 YPL086C 0 SL Pol II transcriptionDEP1 ELP4 YPL101W 1 SL Pol II transcriptionDEP1 KRE24 YPL102C 1 SL UnknownDEP1 YPL144W YPL144W 0 SS MeiosisDEP1 NIP100 YPL174C 1 SL MitosisDEP1 EAF3 YPR023C 1 SS Pol II TranscriptionCTI6 SWC1 YAL011W 1 SL UnknownCTI6 SIF2 YBR103W 1 SS Chromatin/chromosome structureCTI6 AOR1 YBR231C 1 SL SL UnknownCTI6 THI3 YDL080C 1 SS SS Amino-acid metabolismCTI6 SWR1 YDR334W 1 SL UnknownCTI6 VPS72 YDR485C 1 SL Vesicular transportCTI6 HOS2 YGL194C 1 SS Chromatin/chromosome structureCTI6 PAC10 YGR078C 1 SS Cell structureCTI6 TIM13 YGR181W 1 SS SS Protein translocationCTI6 YGR182C YGR182C 1 SL SS UnknownCTI6 ARP6 YLR085C 1 SS Cell structureCTI6 CDC73 YLR418C 1 SL Pol II transcriptionCTI6 VPS71 YML041C 1 SS Vesicular transportCTI6 PRM6 YML047C 1 SL UnknownCTI6 HTZ1 YOL012C 1 SL Chromatin/chromosome structureCTI6 LEO1 YOR123C 1 SS SS Chromatin/chromosome structureSAP30 VPS8 YAL002W 1 SS Vesicular transportSAP30 SWC1 YAL011W 1 SL UnknownSAP30 LTE1 YAL024C 1 SS Cell cycle controlSAP30 SIF2 YBR103W 1 SS Chromatin/chromosome structureSAP30 AOR1 YBR231C 1 SL Unknown

Page 110: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

SAP30 NHP10 YDL002C 1 SS SS UnknownSAP30 YDL033C YDL033C 1 SL SS UnknownSAP30 BRE1 YDL074C 1 SS Chromatin/chromosome stuctureSAP30 THI3 YDL080C 1 SL Amino-acid metabolismSAP30 SWR1 YDR334W 1 SL UnknownSAP30 SPT3 YDR392W 1 SS Chromatin/chromosome stuctureSAP30 VPS72 YDR485C 1 SL Vesicular transportSAP30 BIM1 YER016W 1 SS MitosisSAP30 RMD7 YER083C 1 SS SL Cell wall organization and biogenesisSAP30 IES5 YER092W 1 SS SS UnknownSAP30 SWI4 YER111C 1 SS Cell cycle controlSAP30 YER139C YER139C 1 SS SS UnknownSAP30 SOH1 YGL127C 1 SS DNA repairSAP30 YIP5 YGL161C 1 SS SS Vesicular transportSAP30 HOS2 YGL194C 1 SS Chromatin/chromosome structureSAP30 RTF1 YGL244W 1 SS Pol II transcriptionSAP30 TIM13 YGR181W 1 SL Protein translocationSAP30 YGR182C YGR182C 1 SL SL UnknownSAP30 STB5 YHR178W 1 SL Pol II transcriptionSAP30 RPN10 YHR200W 1 SL Pol II transcriptionSAP30 ASF1 YJL115W 1 SS Chromatin/chromosome structureSAP30 SET2 YJL168C 1 SS Chromatin/chromosome structureSAP30 SET3 YKR029C 1 SS Chromatin/chromosome structureSAP30 SPT8 YLR055C 1 SS Chromatin/chromosome structureSAP30 ARP6 YLR085C 1 SL Cell structureSAP30 SEC22 YLR268W 1 SS Vesicular transportSAP30 VRP1 YLR337C 1 SS SL Cell polaritySAP30 CDC73 YLR418C 1 SL Pol II transcriptionSAP30 VPS71 YML041C 1 SL Vesicular transportSAP30 PRM6 YML047C 1 SL UnknownSAP30 VPS9 YML097C 1 SS Vesicular transportSAP30 MRE11 YMR224C 1 SS DNA repairSAP30 TOM70 YNL121C 1 SS SS Small molecule transportSAP30 YNL140C YNL140C 1 SS UnknownSAP30 YNL171C YNL171C 1 SL UnknownSAP30 IES2 YNL215W 1 SL SS UnknownSAP30 CLA4 YNL298W 1 SL Cell polaritySAP30 HTZ1 YOL012C 1 SL Chromatin/chromosome structureSAP30 LEO1 YOR123C 1 SS Chromatin/chromosome structureSAP30 SAS5 YOR213C 1 SS SS Chromatin/chromosome structureSAP30 SNU66 YOR308C 1 SS SS RNA splicingSAP30 LGE1 YPL055C 1 SL Cell cycle controlSAP30 ELP3 YPL086C 1 SS Pol II transcriptionSAP30 NIP100 YPL174C 1 SS MitosisCDC42-118 LTE1 YAL024C 2 SL Cell cycle control Kozminski, 2003CDC42-118 YBR077C YBR077C 2 SL Unknown Kozminski, 2003CDC42-118 SEC66 YBR171W 3 SL Vesicular transport Kozminski, 2003CDC42-118 BEM1 YBR200W 0 SL Cell polarity Kozminski, 2003CDC42-118 PAT1 YCR077C 0 SS Chromatin/chromosome structure Kozminski, 2003CDC42-118 SWF1 YDR126W 2 SS Unknown Kozminski, 2003CDC42-118 SSD1 YDR293C 3 SS SS Cell cycle control Kozminski, 2003CDC42-118 GIC2 YDR309C 3 SS Cell polarity Kozminski, 2003CDC42-118 SUM1 YDR310C 3 SS Chromatin/chromosome structure Kozminski, 2003CDC42-118 SWI4 YER111C 3 SS SL Cell cycle control Kozminski, 2003CDC42-118 PEA2 YER149C 3 SL Cell polarity Kozminski, 2003CDC42-118 PMR1 YGL167C 2 SS SL Small molecule transport Kozminski, 2003CDC42-118 HUR1 YGL168W 2 SS Unknown Kozminski, 2003CDC42-118 YGL211W YGL211W 2 SS Unknown Kozminski, 2003CDC42-118 YGR151C YGR151C 3 SL Cell polarity Kozminski, 2003CDC42-118 RSR1 YGR152C 3 SS Cell polarity Kozminski, 2003CDC42-118 ELP2 YGR200C 2 SS Pol II transcription Kozminski, 2003

Page 111: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

CDC42-118 UBA4 YHR111W 2 SS Protein modification Kozminski, 2003CDC42-118 CAP2 YIL034C 2 SS Cell structure Kozminski, 2003CDC42-118 CAP1 YKL007W 0 SS Cell structure Kozminski, 2003CDC42-118 SPA2 YLL021W 2 SS Cell polarity Kozminski, 2003CDC42-118 BUD6 YLR319C 3 SS Cell polarity Kozminski, 2003CDC42-118 ELP6 YMR312W 2 SS Pol II transcription Kozminski, 2003CDC42-118 BNI1 YNL271C 0 SL Cell polarity Kozminski, 2003CDC42-118 MSB3 YNL293W 2 SS Cell polarity Kozminski, 2003CDC42-118 CLA4 YNL298W 2 SL Cell polarity Kozminski, 2003CDC42-118 MSB1 YOR188W 0 SS Cell polarity Kozminski, 2003CDC42-118 ELP3 YPL086C 0 SS Pol II transcription Kozminski, 2003CDC42-118 ELP4 YPL101W 2 SS Pol II transcription Kozminski, 2003CDC42-118 BEM4 YPL161C 3 SL Cell polarity Kozminski, 2003SWF1 ARL1 YBR164C 0 SS Vesicular transportSWF1 PER1 YCR044C 0 SS Other metabolismSWF1 YDL133W YDL133W 0 SL SL UnknownSWF1 CUP5 YEL027W 0 SS SS Vacuole organization and biogenesisSWF1 SPF1 YEL031W 0 SS Small molecule transportSWF1 RMD7 YER083C 0 SS Cell wall organization and biogenesisSWF1 COG7 YGL005C 0 SS Vesicular transportSWF1 YGL007W YGL007W 0 SS SS UnknownSWF1 VMA21 YGR105W 0 SS Vacuolar organization and biogenesisSWF1 YGR228W YGR228W 0 SS UnknownSWF1 SMI1 YGR229C 0 SS Cell wall organization and biogenesisSWF1 GOS1 YHL031C 0 SS Vesicular transportSWF1 YHR151C YHR151C 0 SS SS UnknownSWF1 SYS1 YJL004C 0 SS Protein translocationSWF1 SNX4 YJL036W 0 SL Protein degradationSWF1 BCK1 YJL095W 0 SL Cell wall organization and biogenesisSWF1 KTI12 YKL110C 0 SS UnknownSWF1 YKL118W YKL118W 0 SS SL UnknownSWF1 VPS1 YKR001C 0 SS Vesicular transportSWF1 SPO14 YKR031C 0 SL MeiosisSWF1 YKR033C YKR033C 0 SS SS UnknownSWF1 RIC1 YLR039C 0 SL Vesicular transportSWF1 YPT6 YLR262C 0 SL Vesicular transportSWF1 VID22 YLR373C 0 SL Vacuolar organization and biogenesisSWF1 YLR374C YLR374C 0 SL SS UnknownSWF1 IKI3 YLR384C 0 SS SS Pol II transcriptionSWF1 COG8 YML071C 0 SL Vesicular transportSWF1 HSC82 YMR186W 0 SL Protein foldingSWF1 ELP6 YMR312W 0 SL SS Pol II transcriptionSWF1 COG6 YNL041C 0 SS Vesicular transportSWF1 COG5 YNL051W 0 SS Vesicular transportSWF1 PDR17 YNL264C 0 SL Vesicular transportSWF1 MSO1 YNR049C 0 SL SecretionSWF1 TLG2 YOL018C 0 SS Vesicular transportSWF1 MSB4 YOL112W 0 SL Cell polaritySWF1 OST3 YOR085W 0 SS Protein modificationSWF1 SNC2 YOR327C 0 SL Vesicular transportSWF1 ARL3 YPL051W 0 SS Vesicular transportSWF1 BTS1 YPL069C 0 SL SL Protein modificationSWF1 ELP4 YPL101W 0 SS SS Pol II transcriptionSWF1 KRE24 YPL102C 0 SS UnknownSWF1 BEM4 YPL161C 0 SS Cell polaritySWF1 SSO1 YPL232W 0 SL Vesicular transport

Page 112: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

The "Query Gene" column indicates the gene used as query in a SGA screen.The "Genetic Interaction - Gene Name" column indicates the gene being tested for genetic interaction with a particular query.The "Genetic Interaction - Systematic Name" column indicates the systematic (ORF) name that corresponds to the gene being tested for genetic interaction.The "Result" column contains the result as confirmed by the spot assay version of random spore analysis."Y" refers to synthetic genetic interaction."N" refers to no synthetic genetic interaction."N/D" refers to test not done.

Query Gene

Genetic Interaction - Gene Name

Genetic Interaction - Systematic Name Result

AOR1 ARP1 YHR129C NAOR1 ARP6 YLR085C NAOR1 ASE1 YOR058C NAOR1 BEM1 YBR200W NAOR1 BFA1 YJR053W NAOR1 BIK1 YCL029C NAOR1 BIM1 YER016W YAOR1 BUB1 YGR188C YAOR1 BUB2 YMR055C NAOR1 BUB3 YOR026W YAOR1 CHL4 YDR254W NAOR1 CSM3 YMR048W NAOR1 CTF19 YPL018W NAOR1 CTF3 YLR381W NAOR1 CTF8 YHR191C NAOR1 DCC1 YCL016C NAOR1 DYN1 YKR054C NAOR1 ELP2 YGR200C NAOR1 FAB1 YFR019W NAOR1 GIM3 YNL153C YAOR1 GIM4 YEL003W YAOR1 GIM5 YML094W YAOR1 IES2 YNL215W NAOR1 IML3 YBR107C NAOR1 INP52 YNL106C NAOR1 JNM1 YMR294W NAOR1 KEM1 YGL173C YAOR1 KIP3 YGL216W NAOR1 MAD1 YGL086W NAOR1 MAD2 YJL030W NAOR1 MAD3 YJL013C NAOR1 MCK1 YNL307C NAOR1 MCM21 YDR318W NAOR1 MCM22 YJR135C NAOR1 MRC1 YCL060C NAOR1 NBP2 YDR162C NAOR1 NUM1 YDR150W NAOR1 PAC1 YOR269W NAOR1 PAC11 YDR488C NAOR1 PHO23 YNL097C YAOR1 PPZ1 YML016C NAOR1 RAD54 YGL163C NAOR1 RTT103 YDR289C NAOR1 SAP30 YMR263W YAOR1 SLK19 YOR195W NAOR1 SMI1 YGR229C NAOR1 VAC14 YLR386W NAOR1 VID22 YLR373C NAOR1 RXT2 RXT2 YAOR1 YDR149C YDR149C NAOR1 YGL211W YGL211W NAOR1 YGL217C YGL217C NAOR1 YML095C-A YML095C-A N

Page 113: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

AOR1 YNL170W YNL170W NAOR1 YPL017C YPL017C NAOR1 YTA7 YGR270W YARP1 AOR1 YBR231C NARP1 ARP6 YLR085C NARP1 ASE1 YOR058C NARP1 BEM1 YBR200W NARP1 BFA1 YJR053W NARP1 BIK1 YCL029C NARP1 BIM1 YER016W YARP1 BUB1 YGR188C NARP1 BUB2 YMR055C NARP1 BUB3 YOR026W NARP1 CHL4 YDR254W NARP1 CSM3 YMR048W NARP1 CTF19 YPL018W NARP1 CTF3 YLR381W NARP1 CTF8 YHR191C NARP1 DCC1 YCL016C NARP1 DYN1 YKR054C NARP1 ELP2 YGR200C NARP1 FAB1 YFR019W YARP1 GIM3 YNL153C YARP1 GIM4 YEL003W NARP1 GIM5 YML094W YARP1 IES2 YNL215W NARP1 IML3 YBR107C NARP1 INP52 YNL106C NARP1 JNM1 YMR294W NARP1 KEM1 YGL173C NARP1 KIP3 YGL216W YARP1 MAD1 YGL086W NARP1 MAD2 YJL030W NARP1 MAD3 YJL013C NARP1 MCK1 YNL307C NARP1 MCM21 YDR318W NARP1 MCM22 YJR135C NARP1 MRC1 YCL060C NARP1 NBP2 YDR162C NARP1 NUM1 YDR150W NARP1 PAC1 YOR269W NARP1 PAC11 YDR488C NARP1 PHO23 YNL097C NARP1 PPZ1 YML016C NARP1 RAD54 YGL163C NARP1 RTT103 YDR289C NARP1 SAP30 YMR263W NARP1 SLK19 YOR195W NARP1 SMI1 YGR229C NARP1 VAC14 YLR386W NARP1 VID22 YLR373C NARP1 RXT2 RXT2 NARP1 YDR149C YDR149C NARP1 YGL211W YGL211W NARP1 YGL217C YGL217C YARP1 YML095C-A YML095C-A NARP1 YNL170W YNL170W NARP1 YPL017C YPL017C NARP1 YTA7 YGR270W NARP6 AOR1 YBR231C NARP6 ARP1 YHR129C NARP6 ASE1 YOR058C NARP6 BEM1 YBR200W NARP6 BFA1 YJR053W NARP6 BIK1 YCL029C NARP6 BIM1 YER016W Y

Page 114: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

ARP6 BUB1 YGR188C YARP6 BUB2 YMR055C NARP6 BUB3 YOR026W YARP6 CHL4 YDR254W NARP6 CSM3 YMR048W NARP6 CTF19 YPL018W NARP6 CTF3 YLR381W NARP6 CTF8 YHR191C NARP6 DCC1 YCL016C NARP6 DYN1 YKR054C NARP6 ELP2 YGR200C NARP6 FAB1 YFR019W NARP6 GIM3 YNL153C YARP6 GIM4 YEL003W YARP6 GIM5 YML094W YARP6 IES2 YNL215W NARP6 IML3 YBR107C NARP6 INP52 YNL106C NARP6 JNM1 YMR294W NARP6 KEM1 YGL173C NARP6 KIP3 YGL216W NARP6 MAD1 YGL086W NARP6 MAD2 YJL030W NARP6 MAD3 YJL013C NARP6 MCK1 YNL307C NARP6 MCM21 YDR318W NARP6 MCM22 YJR135C NARP6 MRC1 YCL060C NARP6 NBP2 YDR162C NARP6 NUM1 YDR150W NARP6 PAC1 YOR269W NARP6 PAC11 YDR488C NARP6 PHO23 YNL097C YARP6 PPZ1 YML016C NARP6 RAD54 YGL163C NARP6 RTT103 YDR289C NARP6 SAP30 YMR263W YARP6 SLK19 YOR195W NARP6 SMI1 YGR229C NARP6 VAC14 YLR386W NARP6 VID22 YLR373C NARP6 RXT2 RXT2 YARP6 YDR149C YDR149C NARP6 YGL211W YGL211W NARP6 YGL217C YGL217C NARP6 YML095C-A YML095C-A NARP6 YNL170W YNL170W NARP6 YPL017C YPL017C NARP6 YTA7 YGR270W YASE1 AOR1 YBR231C NASE1 ARP1 YHR129C YASE1 ARP6 YLR085C NASE1 BEM1 YBR200W NASE1 BFA1 YJR053W NASE1 BIK1 YCL029C YASE1 BIM1 YER016W YASE1 BUB1 YGR188C NASE1 BUB2 YMR055C NASE1 BUB3 YOR026W NASE1 CHL4 YDR254W NASE1 CSM3 YMR048W NASE1 CTF19 YPL018W NASE1 CTF3 YLR381W NASE1 CTF8 YHR191C NASE1 DCC1 YCL016C NASE1 DYN1 YKR054C Y

Page 115: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

ASE1 ELP2 YGR200C NASE1 FAB1 YFR019W YASE1 GIM3 YNL153C YASE1 GIM4 YEL003W NASE1 GIM5 YML094W NASE1 IES2 YNL215W NASE1 IML3 YBR107C NASE1 INP52 YNL106C NASE1 JNM1 YMR294W YASE1 KEM1 YGL173C NASE1 KIP3 YGL216W NASE1 MAD1 YGL086W NASE1 MAD2 YJL030W NASE1 MAD3 YJL013C NASE1 MCK1 YNL307C NASE1 MCM21 YDR318W NASE1 MCM22 YJR135C NASE1 MRC1 YCL060C NASE1 NBP2 YDR162C NASE1 NUM1 YDR150W YASE1 PAC1 YOR269W YASE1 PAC11 YDR488C YASE1 PHO23 YNL097C NASE1 PPZ1 YML016C NASE1 RAD54 YGL163C NASE1 RTT103 YDR289C NASE1 SAP30 YMR263W NASE1 SLK19 YOR195W NASE1 SMI1 YGR229C NASE1 VAC14 YLR386W NASE1 VID22 YLR373C NASE1 RXT2 RXT2 NASE1 YDR149C YDR149C YASE1 YGL211W YGL211W NASE1 YGL217C YGL217C NASE1 YML095C-A YML095C-A NASE1 YNL170W YNL170W NASE1 YPL017C YPL017C NASE1 YTA7 YGR270W NBEM1 AOR1 YBR231C NBEM1 ARP1 YHR129C NBEM1 ARP6 YLR085C NBEM1 ASE1 YOR058C NBEM1 BFA1 YJR053W NBEM1 BIK1 YCL029C NBEM1 BIM1 YER016W YBEM1 BUB1 YGR188C NBEM1 BUB2 YMR055C NBEM1 BUB3 YOR026W NBEM1 CHL4 YDR254W NBEM1 CSM3 YMR048W NBEM1 CTF19 YPL018W NBEM1 CTF3 YLR381W NBEM1 CTF8 YHR191C NBEM1 DCC1 YCL016C NBEM1 DYN1 YKR054C NBEM1 ELP2 YGR200C YBEM1 FAB1 YFR019W YBEM1 GIM3 YNL153C YBEM1 GIM4 YEL003W NBEM1 GIM5 YML094W YBEM1 IES2 YNL215W NBEM1 IML3 YBR107C NBEM1 INP52 YNL106C NBEM1 JNM1 YMR294W NBEM1 KEM1 YGL173C Y

Page 116: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

BEM1 KIP3 YGL216W NBEM1 MAD1 YGL086W NBEM1 MAD2 YJL030W NBEM1 MAD3 YJL013C NBEM1 MCK1 YNL307C YBEM1 MCM21 YDR318W NBEM1 MCM22 YJR135C NBEM1 MRC1 YCL060C NBEM1 NBP2 YDR162C YBEM1 NUM1 YDR150W NBEM1 PAC1 YOR269W NBEM1 PAC11 YDR488C NBEM1 PHO23 YNL097C NBEM1 PPZ1 YML016C YBEM1 RAD54 YGL163C NBEM1 RTT103 YDR289C NBEM1 SAP30 YMR263W NBEM1 SLK19 YOR195W NBEM1 SMI1 YGR229C YBEM1 VAC14 YLR386W NBEM1 VID22 YLR373C YBEM1 RXT2 RXT2 NBEM1 YDR149C YDR149C NBEM1 YGL211W YGL211W YBEM1 YGL217C YGL217C NBEM1 YML095C-A YML095C-A NBEM1 YNL170W YNL170W NBEM1 YPL017C YPL017C NBEM1 YTA7 YGR270W NBFA1 AOR1 YBR231C NBFA1 ARP1 YHR129C NBFA1 ARP6 YLR085C NBFA1 ASE1 YOR058C NBFA1 BEM1 YBR200W NBFA1 BIK1 YCL029C NBFA1 BIM1 YER016W YBFA1 BUB1 YGR188C NBFA1 BUB2 YMR055C NBFA1 BUB3 YOR026W NBFA1 CHL4 YDR254W NBFA1 CSM3 YMR048W NBFA1 CTF19 YPL018W NBFA1 CTF3 YLR381W NBFA1 CTF8 YHR191C NBFA1 DCC1 YCL016C NBFA1 DYN1 YKR054C NBFA1 ELP2 YGR200C NBFA1 FAB1 YFR019W NBFA1 GIM3 YNL153C NBFA1 GIM4 YEL003W NBFA1 GIM5 YML094W NBFA1 IES2 YNL215W NBFA1 IML3 YBR107C NBFA1 INP52 YNL106C NBFA1 JNM1 YMR294W NBFA1 KEM1 YGL173C NBFA1 KIP3 YGL216W NBFA1 MAD1 YGL086W NBFA1 MAD2 YJL030W NBFA1 MAD3 YJL013C NBFA1 MCK1 YNL307C NBFA1 MCM21 YDR318W NBFA1 MCM22 YJR135C NBFA1 MRC1 YCL060C NBFA1 NBP2 YDR162C NBFA1 NUM1 YDR150W N

Page 117: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

BFA1 PAC1 YOR269W NBFA1 PAC11 YDR488C NBFA1 PHO23 YNL097C NBFA1 PPZ1 YML016C NBFA1 RAD54 YGL163C NBFA1 RTT103 YDR289C NBFA1 SAP30 YMR263W NBFA1 SLK19 YOR195W NBFA1 SMI1 YGR229C NBFA1 VAC14 YLR386W NBFA1 VID22 YLR373C NBFA1 RXT2 RXT2 NBFA1 YDR149C YDR149C NBFA1 YGL211W YGL211W NBFA1 YGL217C YGL217C NBFA1 YML095C-A YML095C-A NBFA1 YNL170W YNL170W NBFA1 YPL017C YPL017C NBFA1 YTA7 YGR270W NBIK1 AOR1 YBR231C YBIK1 ARP1 YHR129C NBIK1 ARP6 YLR085C NBIK1 ASE1 YOR058C YBIK1 BEM1 YBR200W NBIK1 BFA1 YJR053W YBIK1 BIM1 YER016W YBIK1 BUB1 YGR188C YBIK1 BUB2 YMR055C NBIK1 BUB3 YOR026W YBIK1 CHL4 YDR254W NBIK1 CSM3 YMR048W NBIK1 CTF19 YPL018W NBIK1 CTF3 YLR381W NBIK1 CTF8 YHR191C NBIK1 DCC1 YCL016C NBIK1 DYN1 YKR054C NBIK1 ELP2 YGR200C NBIK1 FAB1 YFR019W YBIK1 GIM3 YNL153C YBIK1 GIM4 YEL003W NBIK1 GIM5 YML094W YBIK1 IES2 YNL215W NBIK1 IML3 YBR107C NBIK1 INP52 YNL106C YBIK1 JNM1 YMR294W NBIK1 KEM1 YGL173C NBIK1 KIP3 YGL216W NBIK1 MAD1 YGL086W NBIK1 MAD2 YJL030W NBIK1 MAD3 YJL013C NBIK1 MCK1 YNL307C NBIK1 MCM21 YDR318W NBIK1 MCM22 YJR135C NBIK1 MRC1 YCL060C NBIK1 NBP2 YDR162C NBIK1 NUM1 YDR150W NBIK1 PAC1 YOR269W NBIK1 PAC11 YDR488C NBIK1 PHO23 YNL097C NBIK1 PPZ1 YML016C NBIK1 RAD54 YGL163C NBIK1 RTT103 YDR289C YBIK1 SAP30 YMR263W NBIK1 SLK19 YOR195W NBIK1 SMI1 YGR229C NBIK1 VAC14 YLR386W N

Page 118: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

BIK1 VID22 YLR373C NBIK1 RXT2 RXT2 NBIK1 YDR149C YDR149C NBIK1 YGL211W YGL211W NBIK1 YGL217C YGL217C NBIK1 YML095C-A YML095C-A NBIK1 YNL170W YNL170W NBIK1 YPL017C YPL017C NBIK1 YTA7 YGR270W NBIM1 AOR1 YBR231C YBIM1 ARP1 YHR129C YBIM1 ARP6 YLR085C YBIM1 ASE1 YOR058C YBIM1 BEM1 YBR200W YBIM1 BFA1 YJR053W YBIM1 BIK1 YCL029C YBIM1 BUB1 YGR188C YBIM1 BUB2 YMR055C YBIM1 BUB3 YOR026W YBIM1 CHL4 YDR254W YBIM1 CSM3 YMR048W YBIM1 CTF19 YPL018W YBIM1 CTF3 YLR381W YBIM1 CTF8 YHR191C YBIM1 DCC1 YCL016C YBIM1 DYN1 YKR054C YBIM1 ELP2 YGR200C YBIM1 FAB1 YFR019W YBIM1 GIM3 YNL153C YBIM1 GIM4 YEL003W YBIM1 GIM5 YML094W YBIM1 IES2 YNL215W YBIM1 IML3 YBR107C YBIM1 INP52 YNL106C YBIM1 JNM1 YMR294W YBIM1 KEM1 YGL173C YBIM1 KIP3 YGL216W YBIM1 MAD1 YGL086W YBIM1 MAD2 YJL030W YBIM1 MAD3 YJL013C YBIM1 MCK1 YNL307C YBIM1 MCM21 YDR318W YBIM1 MCM22 YJR135C YBIM1 MRC1 YCL060C YBIM1 NBP2 YDR162C YBIM1 NUM1 YDR150W YBIM1 PAC1 YOR269W YBIM1 PAC11 YDR488C YBIM1 PHO23 YNL097C YBIM1 PPZ1 YML016C YBIM1 RAD54 YGL163C YBIM1 RTT103 YDR289C YBIM1 SAP30 YMR263W YBIM1 SLK19 YOR195W YBIM1 SMI1 YGR229C YBIM1 VAC14 YLR386W YBIM1 VID22 YLR373C YBIM1 RXT2 RXT2 YBIM1 YDR149C YDR149C YBIM1 YGL211W YGL211W YBIM1 YGL217C YGL217C YBIM1 YML095C-A YML095C-A YBIM1 YNL170W YNL170W YBIM1 YPL017C YPL017C YBIM1 YTA7 YGR270W YBUB1 AOR1 YBR231C N/D

Page 119: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

BUB1 ARP1 YHR129C N/DBUB1 ARP6 YLR085C N/DBUB1 ASE1 YOR058C N/DBUB1 BEM1 YBR200W N/DBUB1 BFA1 YJR053W N/DBUB1 BIK1 YCL029C N/DBUB1 BIM1 YER016W N/DBUB1 BUB2 YMR055C N/DBUB1 BUB3 YOR026W N/DBUB1 CHL4 YDR254W N/DBUB1 CSM3 YMR048W N/DBUB1 CTF19 YPL018W N/DBUB1 CTF3 YLR381W N/DBUB1 CTF8 YHR191C N/DBUB1 DCC1 YCL016C N/DBUB1 DYN1 YKR054C N/DBUB1 ELP2 YGR200C N/DBUB1 FAB1 YFR019W N/DBUB1 GIM3 YNL153C N/DBUB1 GIM4 YEL003W N/DBUB1 GIM5 YML094W N/DBUB1 IES2 YNL215W N/DBUB1 IML3 YBR107C N/DBUB1 INP52 YNL106C N/DBUB1 JNM1 YMR294W N/DBUB1 KEM1 YGL173C N/DBUB1 KIP3 YGL216W N/DBUB1 MAD1 YGL086W N/DBUB1 MAD2 YJL030W N/DBUB1 MAD3 YJL013C N/DBUB1 MCK1 YNL307C N/DBUB1 MCM21 YDR318W N/DBUB1 MCM22 YJR135C N/DBUB1 MRC1 YCL060C N/DBUB1 NBP2 YDR162C N/DBUB1 NUM1 YDR150W N/DBUB1 PAC1 YOR269W N/DBUB1 PAC11 YDR488C N/DBUB1 PHO23 YNL097C N/DBUB1 PPZ1 YML016C N/DBUB1 RAD54 YGL163C N/DBUB1 RTT103 YDR289C N/DBUB1 SAP30 YMR263W N/DBUB1 SLK19 YOR195W N/DBUB1 SMI1 YGR229C N/DBUB1 VAC14 YLR386W N/DBUB1 VID22 YLR373C N/DBUB1 RXT2 RXT2 N/DBUB1 YDR149C YDR149C N/DBUB1 YGL211W YGL211W N/DBUB1 YGL217C YGL217C N/DBUB1 YML095C-A YML095C-A N/DBUB1 YNL170W YNL170W N/DBUB1 YPL017C YPL017C N/DBUB1 YTA7 YGR270W N/DBUB2 AOR1 YBR231C NBUB2 ARP1 YHR129C NBUB2 ARP6 YLR085C NBUB2 ASE1 YOR058C NBUB2 BEM1 YBR200W NBUB2 BFA1 YJR053W NBUB2 BIK1 YCL029C NBUB2 BIM1 YER016W YBUB2 BUB1 YGR188C NBUB2 BUB3 YOR026W NBUB2 CHL4 YDR254W N

Page 120: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

BUB2 CSM3 YMR048W YBUB2 CTF19 YPL018W NBUB2 CTF3 YLR381W NBUB2 CTF8 YHR191C NBUB2 DCC1 YCL016C NBUB2 DYN1 YKR054C NBUB2 ELP2 YGR200C NBUB2 FAB1 YFR019W NBUB2 GIM3 YNL153C YBUB2 GIM4 YEL003W YBUB2 GIM5 YML094W YBUB2 IES2 YNL215W NBUB2 IML3 YBR107C NBUB2 INP52 YNL106C NBUB2 JNM1 YMR294W NBUB2 KEM1 YGL173C NBUB2 KIP3 YGL216W NBUB2 MAD1 YGL086W NBUB2 MAD2 YJL030W NBUB2 MAD3 YJL013C NBUB2 MCK1 YNL307C NBUB2 MCM21 YDR318W NBUB2 MCM22 YJR135C NBUB2 MRC1 YCL060C NBUB2 NBP2 YDR162C NBUB2 NUM1 YDR150W YBUB2 PAC1 YOR269W NBUB2 PAC11 YDR488C NBUB2 PHO23 YNL097C NBUB2 PPZ1 YML016C NBUB2 RAD54 YGL163C NBUB2 RTT103 YDR289C NBUB2 SAP30 YMR263W NBUB2 SLK19 YOR195W NBUB2 SMI1 YGR229C NBUB2 VAC14 YLR386W NBUB2 VID22 YLR373C NBUB2 RXT2 RXT2 NBUB2 YDR149C YDR149C NBUB2 YGL211W YGL211W NBUB2 YGL217C YGL217C NBUB2 YML095C-A YML095C-A NBUB2 YNL170W YNL170W NBUB2 YPL017C YPL017C NBUB2 YTA7 YGR270W NBUB3 AOR1 YBR231C NBUB3 ARP1 YHR129C NBUB3 ARP6 YLR085C YBUB3 ASE1 YOR058C YBUB3 BEM1 YBR200W NBUB3 BFA1 YJR053W NBUB3 BIK1 YCL029C YBUB3 BIM1 YER016W YBUB3 BUB1 YGR188C NBUB3 BUB2 YMR055C NBUB3 CHL4 YDR254W YBUB3 CSM3 YMR048W YBUB3 CTF19 YPL018W YBUB3 CTF3 YLR381W YBUB3 CTF8 YHR191C NBUB3 DCC1 YCL016C NBUB3 DYN1 YKR054C NBUB3 ELP2 YGR200C NBUB3 FAB1 YFR019W NBUB3 GIM3 YNL153C YBUB3 GIM4 YEL003W Y

Page 121: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

BUB3 GIM5 YML094W YBUB3 IES2 YNL215W YBUB3 IML3 YBR107C YBUB3 INP52 YNL106C NBUB3 JNM1 YMR294W NBUB3 KEM1 YGL173C YBUB3 KIP3 YGL216W YBUB3 MAD1 YGL086W NBUB3 MAD2 YJL030W NBUB3 MAD3 YJL013C NBUB3 MCK1 YNL307C NBUB3 MCM21 YDR318W YBUB3 MCM22 YJR135C YBUB3 MRC1 YCL060C NBUB3 NBP2 YDR162C NBUB3 NUM1 YDR150W NBUB3 PAC1 YOR269W NBUB3 PAC11 YDR488C NBUB3 PHO23 YNL097C NBUB3 PPZ1 YML016C NBUB3 RAD54 YGL163C NBUB3 RTT103 YDR289C NBUB3 SAP30 YMR263W NBUB3 SLK19 YOR195W YBUB3 SMI1 YGR229C NBUB3 VAC14 YLR386W YBUB3 VID22 YLR373C YBUB3 RXT2 RXT2 NBUB3 YDR149C YDR149C NBUB3 YGL211W YGL211W NBUB3 YGL217C YGL217C YBUB3 YML095C-A YML095C-A NBUB3 YNL170W YNL170W NBUB3 YPL017C YPL017C NBUB3 YTA7 YGR270W YCHL4 AOR1 YBR231C NCHL4 ARP1 YHR129C NCHL4 ARP6 YLR085C NCHL4 ASE1 YOR058C NCHL4 BEM1 YBR200W NCHL4 BFA1 YJR053W NCHL4 BIK1 YCL029C NCHL4 BIM1 YER016W YCHL4 BUB1 YGR188C YCHL4 BUB2 YMR055C NCHL4 BUB3 YOR026W YCHL4 CSM3 YMR048W NCHL4 CTF19 YPL018W NCHL4 CTF3 YLR381W NCHL4 CTF8 YHR191C NCHL4 DCC1 YCL016C NCHL4 DYN1 YKR054C NCHL4 ELP2 YGR200C NCHL4 FAB1 YFR019W NCHL4 GIM3 YNL153C NCHL4 GIM4 YEL003W NCHL4 GIM5 YML094W YCHL4 IES2 YNL215W NCHL4 IML3 YBR107C NCHL4 INP52 YNL106C NCHL4 JNM1 YMR294W NCHL4 KEM1 YGL173C YCHL4 KIP3 YGL216W NCHL4 MAD1 YGL086W YCHL4 MAD2 YJL030W YCHL4 MAD3 YJL013C N

Page 122: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

CHL4 MCK1 YNL307C NCHL4 MCM21 YDR318W NCHL4 MCM22 YJR135C NCHL4 MRC1 YCL060C NCHL4 NBP2 YDR162C NCHL4 NUM1 YDR150W NCHL4 PAC1 YOR269W NCHL4 PAC11 YDR488C NCHL4 PHO23 YNL097C NCHL4 PPZ1 YML016C NCHL4 RAD54 YGL163C NCHL4 RTT103 YDR289C YCHL4 SAP30 YMR263W NCHL4 SLK19 YOR195W NCHL4 SMI1 YGR229C NCHL4 VAC14 YLR386W NCHL4 VID22 YLR373C NCHL4 RXT2 RXT2 NCHL4 YDR149C YDR149C NCHL4 YGL211W YGL211W NCHL4 YGL217C YGL217C NCHL4 YML095C-A YML095C-A NCHL4 YNL170W YNL170W NCHL4 YPL017C YPL017C NCHL4 YTA7 YGR270W NCSM3 AOR1 YBR231C NCSM3 ARP1 YHR129C NCSM3 ARP6 YLR085C NCSM3 ASE1 YOR058C NCSM3 BEM1 YBR200W NCSM3 BFA1 YJR053W NCSM3 BIK1 YCL029C NCSM3 BIM1 YER016W YCSM3 BUB1 YGR188C YCSM3 BUB2 YMR055C YCSM3 BUB3 YOR026W YCSM3 CHL4 YDR254W NCSM3 CTF19 YPL018W NCSM3 CTF3 YLR381W NCSM3 CTF8 YHR191C YCSM3 DCC1 YCL016C YCSM3 DYN1 YKR054C NCSM3 ELP2 YGR200C NCSM3 FAB1 YFR019W NCSM3 GIM3 YNL153C NCSM3 GIM4 YEL003W NCSM3 GIM5 YML094W NCSM3 IES2 YNL215W NCSM3 IML3 YBR107C NCSM3 INP52 YNL106C NCSM3 JNM1 YMR294W NCSM3 KEM1 YGL173C NCSM3 KIP3 YGL216W NCSM3 MAD1 YGL086W NCSM3 MAD2 YJL030W NCSM3 MAD3 YJL013C NCSM3 MCK1 YNL307C NCSM3 MCM21 YDR318W NCSM3 MCM22 YJR135C NCSM3 MRC1 YCL060C YCSM3 NBP2 YDR162C NCSM3 NUM1 YDR150W NCSM3 PAC1 YOR269W NCSM3 PAC11 YDR488C NCSM3 PHO23 YNL097C NCSM3 PPZ1 YML016C N

Page 123: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

CSM3 RAD54 YGL163C NCSM3 RTT103 YDR289C NCSM3 SAP30 YMR263W NCSM3 SLK19 YOR195W NCSM3 SMI1 YGR229C NCSM3 VAC14 YLR386W NCSM3 VID22 YLR373C NCSM3 RXT2 RXT2 NCSM3 YDR149C YDR149C NCSM3 YGL211W YGL211W NCSM3 YGL217C YGL217C NCSM3 YML095C-A YML095C-A NCSM3 YNL170W YNL170W NCSM3 YPL017C YPL017C NCSM3 YTA7 YGR270W NCTF19 AOR1 YBR231C NCTF19 ARP1 YHR129C NCTF19 ARP6 YLR085C NCTF19 ASE1 YOR058C NCTF19 BEM1 YBR200W NCTF19 BFA1 YJR053W NCTF19 BIK1 YCL029C NCTF19 BIM1 YER016W YCTF19 BUB1 YGR188C YCTF19 BUB2 YMR055C NCTF19 BUB3 YOR026W YCTF19 CHL4 YDR254W NCTF19 CSM3 YMR048W NCTF19 CTF3 YLR381W NCTF19 CTF8 YHR191C NCTF19 DCC1 YCL016C NCTF19 DYN1 YKR054C NCTF19 ELP2 YGR200C NCTF19 FAB1 YFR019W NCTF19 GIM3 YNL153C YCTF19 GIM4 YEL003W NCTF19 GIM5 YML094W YCTF19 IES2 YNL215W NCTF19 IML3 YBR107C NCTF19 INP52 YNL106C YCTF19 JNM1 YMR294W NCTF19 KEM1 YGL173C NCTF19 KIP3 YGL216W NCTF19 MAD1 YGL086W YCTF19 MAD2 YJL030W YCTF19 MAD3 YJL013C NCTF19 MCK1 YNL307C NCTF19 MCM21 YDR318W NCTF19 MCM22 YJR135C NCTF19 MRC1 YCL060C NCTF19 NBP2 YDR162C NCTF19 NUM1 YDR150W NCTF19 PAC1 YOR269W NCTF19 PAC11 YDR488C NCTF19 PHO23 YNL097C NCTF19 PPZ1 YML016C NCTF19 RAD54 YGL163C NCTF19 RTT103 YDR289C NCTF19 SAP30 YMR263W NCTF19 SLK19 YOR195W NCTF19 SMI1 YGR229C NCTF19 VAC14 YLR386W NCTF19 VID22 YLR373C NCTF19 RXT2 RXT2 NCTF19 YDR149C YDR149C NCTF19 YGL211W YGL211W N

Page 124: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

CTF19 YGL217C YGL217C NCTF19 YML095C-A YML095C-A NCTF19 YNL170W YNL170W NCTF19 YPL017C YPL017C YCTF19 YTA7 YGR270W NCTF3 AOR1 YBR231C NCTF3 ARP1 YHR129C NCTF3 ARP6 YLR085C NCTF3 ASE1 YOR058C NCTF3 BEM1 YBR200W NCTF3 BFA1 YJR053W NCTF3 BIK1 YCL029C NCTF3 BIM1 YER016W YCTF3 BUB1 YGR188C YCTF3 BUB2 YMR055C NCTF3 BUB3 YOR026W NCTF3 CHL4 YDR254W NCTF3 CSM3 YMR048W NCTF3 CTF19 YPL018W NCTF3 CTF8 YHR191C NCTF3 DCC1 YCL016C NCTF3 DYN1 YKR054C NCTF3 ELP2 YGR200C NCTF3 FAB1 YFR019W YCTF3 GIM3 YNL153C NCTF3 GIM4 YEL003W NCTF3 GIM5 YML094W NCTF3 IES2 YNL215W NCTF3 IML3 YBR107C NCTF3 INP52 YNL106C YCTF3 JNM1 YMR294W NCTF3 KEM1 YGL173C NCTF3 KIP3 YGL216W NCTF3 MAD1 YGL086W NCTF3 MAD2 YJL030W NCTF3 MAD3 YJL013C NCTF3 MCK1 YNL307C NCTF3 MCM21 YDR318W NCTF3 MCM22 YJR135C NCTF3 MRC1 YCL060C NCTF3 NBP2 YDR162C NCTF3 NUM1 YDR150W NCTF3 PAC1 YOR269W NCTF3 PAC11 YDR488C NCTF3 PHO23 YNL097C NCTF3 PPZ1 YML016C NCTF3 RAD54 YGL163C NCTF3 RTT103 YDR289C NCTF3 SAP30 YMR263W NCTF3 SLK19 YOR195W NCTF3 SMI1 YGR229C NCTF3 VAC14 YLR386W YCTF3 VID22 YLR373C YCTF3 RXT2 RXT2 NCTF3 YDR149C YDR149C NCTF3 YGL211W YGL211W NCTF3 YGL217C YGL217C NCTF3 YML095C-A YML095C-A YCTF3 YNL170W YNL170W NCTF3 YPL017C YPL017C NCTF3 YTA7 YGR270W NCTF8 AOR1 YBR231C NCTF8 ARP1 YHR129C NCTF8 ARP6 YLR085C NCTF8 ASE1 YOR058C NCTF8 BEM1 YBR200W N

Page 125: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

CTF8 BFA1 YJR053W NCTF8 BIK1 YCL029C NCTF8 BIM1 YER016W YCTF8 BUB1 YGR188C YCTF8 BUB2 YMR055C NCTF8 BUB3 YOR026W NCTF8 CHL4 YDR254W NCTF8 CSM3 YMR048W YCTF8 CTF19 YPL018W NCTF8 CTF3 YLR381W NCTF8 DCC1 YCL016C NCTF8 DYN1 YKR054C NCTF8 ELP2 YGR200C NCTF8 FAB1 YFR019W NCTF8 GIM3 YNL153C YCTF8 GIM4 YEL003W NCTF8 GIM5 YML094W YCTF8 IES2 YNL215W NCTF8 IML3 YBR107C NCTF8 INP52 YNL106C YCTF8 JNM1 YMR294W NCTF8 KEM1 YGL173C NCTF8 KIP3 YGL216W NCTF8 MAD1 YGL086W NCTF8 MAD2 YJL030W NCTF8 MAD3 YJL013C NCTF8 MCK1 YNL307C NCTF8 MCM21 YDR318W NCTF8 MCM22 YJR135C NCTF8 MRC1 YCL060C YCTF8 NBP2 YDR162C NCTF8 NUM1 YDR150W NCTF8 PAC1 YOR269W NCTF8 PAC11 YDR488C NCTF8 PHO23 YNL097C NCTF8 PPZ1 YML016C NCTF8 RAD54 YGL163C NCTF8 RTT103 YDR289C NCTF8 SAP30 YMR263W NCTF8 SLK19 YOR195W NCTF8 SMI1 YGR229C NCTF8 VAC14 YLR386W NCTF8 VID22 YLR373C NCTF8 RXT2 RXT2 NCTF8 YDR149C YDR149C NCTF8 YGL211W YGL211W NCTF8 YGL217C YGL217C NCTF8 YML095C-A YML095C-A NCTF8 YNL170W YNL170W NCTF8 YPL017C YPL017C NCTF8 YTA7 YGR270W NDCC1 AOR1 YBR231C NDCC1 ARP1 YHR129C NDCC1 ARP6 YLR085C NDCC1 ASE1 YOR058C NDCC1 BEM1 YBR200W NDCC1 BFA1 YJR053W NDCC1 BIK1 YCL029C YDCC1 BIM1 YER016W YDCC1 BUB1 YGR188C YDCC1 BUB2 YMR055C NDCC1 BUB3 YOR026W YDCC1 CHL4 YDR254W NDCC1 CSM3 YMR048W YDCC1 CTF19 YPL018W NDCC1 CTF3 YLR381W N

Page 126: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

DCC1 CTF8 YHR191C NDCC1 DYN1 YKR054C NDCC1 ELP2 YGR200C NDCC1 FAB1 YFR019W YDCC1 GIM3 YNL153C YDCC1 GIM4 YEL003W NDCC1 GIM5 YML094W YDCC1 IES2 YNL215W NDCC1 IML3 YBR107C NDCC1 INP52 YNL106C YDCC1 JNM1 YMR294W NDCC1 KEM1 YGL173C YDCC1 KIP3 YGL216W YDCC1 MAD1 YGL086W NDCC1 MAD2 YJL030W NDCC1 MAD3 YJL013C NDCC1 MCK1 YNL307C NDCC1 MCM21 YDR318W YDCC1 MCM22 YJR135C NDCC1 MRC1 YCL060C YDCC1 NBP2 YDR162C NDCC1 NUM1 YDR150W NDCC1 PAC1 YOR269W NDCC1 PAC11 YDR488C NDCC1 PHO23 YNL097C YDCC1 PPZ1 YML016C NDCC1 RAD54 YGL163C NDCC1 RTT103 YDR289C NDCC1 SAP30 YMR263W YDCC1 SLK19 YOR195W NDCC1 SMI1 YGR229C YDCC1 VAC14 YLR386W NDCC1 VID22 YLR373C NDCC1 RXT2 RXT2 NDCC1 YDR149C YDR149C NDCC1 YGL211W YGL211W NDCC1 YGL217C YGL217C NDCC1 YML095C-A YML095C-A YDCC1 YNL170W YNL170W NDCC1 YPL017C YPL017C NDCC1 YTA7 YGR270W NDYN1 AOR1 YBR231C NDYN1 ARP1 YHR129C NDYN1 ARP6 YLR085C NDYN1 ASE1 YOR058C NDYN1 BEM1 YBR200W NDYN1 BFA1 YJR053W NDYN1 BIK1 YCL029C NDYN1 BIM1 YER016W YDYN1 BUB1 YGR188C NDYN1 BUB2 YMR055C NDYN1 BUB3 YOR026W NDYN1 CHL4 YDR254W NDYN1 CSM3 YMR048W NDYN1 CTF19 YPL018W NDYN1 CTF3 YLR381W NDYN1 CTF8 YHR191C NDYN1 DCC1 YCL016C NDYN1 ELP2 YGR200C NDYN1 FAB1 YFR019W YDYN1 GIM3 YNL153C YDYN1 GIM4 YEL003W NDYN1 GIM5 YML094W YDYN1 IES2 YNL215W NDYN1 IML3 YBR107C NDYN1 INP52 YNL106C N

Page 127: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

DYN1 JNM1 YMR294W NDYN1 KEM1 YGL173C NDYN1 KIP3 YGL216W YDYN1 MAD1 YGL086W NDYN1 MAD2 YJL030W NDYN1 MAD3 YJL013C NDYN1 MCK1 YNL307C NDYN1 MCM21 YDR318W NDYN1 MCM22 YJR135C NDYN1 MRC1 YCL060C NDYN1 NBP2 YDR162C NDYN1 NUM1 YDR150W NDYN1 PAC1 YOR269W NDYN1 PAC11 YDR488C NDYN1 PHO23 YNL097C NDYN1 PPZ1 YML016C NDYN1 RAD54 YGL163C NDYN1 RTT103 YDR289C NDYN1 SAP30 YMR263W NDYN1 SLK19 YOR195W NDYN1 SMI1 YGR229C NDYN1 VAC14 YLR386W NDYN1 VID22 YLR373C NDYN1 RXT2 RXT2 NDYN1 YDR149C YDR149C NDYN1 YGL211W YGL211W NDYN1 YGL217C YGL217C YDYN1 YML095C-A YML095C-A NDYN1 YNL170W YNL170W NDYN1 YPL017C YPL017C NDYN1 YTA7 YGR270W NELP2 AOR1 YBR231C NELP2 ARP1 YHR129C NELP2 ARP6 YLR085C NELP2 ASE1 YOR058C NELP2 BEM1 YBR200W YELP2 BFA1 YJR053W NELP2 BIK1 YCL029C NELP2 BIM1 YER016W YELP2 BUB1 YGR188C YELP2 BUB2 YMR055C NELP2 BUB3 YOR026W YELP2 CHL4 YDR254W NELP2 CSM3 YMR048W NELP2 CTF19 YPL018W NELP2 CTF3 YLR381W NELP2 CTF8 YHR191C NELP2 DCC1 YCL016C NELP2 DYN1 YKR054C NELP2 FAB1 YFR019W NELP2 GIM3 YNL153C NELP2 GIM4 YEL003W NELP2 GIM5 YML094W NELP2 IES2 YNL215W NELP2 IML3 YBR107C NELP2 INP52 YNL106C NELP2 JNM1 YMR294W NELP2 KEM1 YGL173C NELP2 KIP3 YGL216W NELP2 MAD1 YGL086W NELP2 MAD2 YJL030W NELP2 MAD3 YJL013C NELP2 MCK1 YNL307C NELP2 MCM21 YDR318W NELP2 MCM22 YJR135C NELP2 MRC1 YCL060C N

Page 128: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

ELP2 NBP2 YDR162C YELP2 NUM1 YDR150W NELP2 PAC1 YOR269W NELP2 PAC11 YDR488C NELP2 PHO23 YNL097C NELP2 PPZ1 YML016C NELP2 RAD54 YGL163C NELP2 RTT103 YDR289C NELP2 SAP30 YMR263W NELP2 SLK19 YOR195W NELP2 SMI1 YGR229C YELP2 VAC14 YLR386W NELP2 VID22 YLR373C NELP2 RXT2 RXT2 NELP2 YDR149C YDR149C NELP2 YGL211W YGL211W YELP2 YGL217C YGL217C NELP2 YML095C-A YML095C-A NELP2 YNL170W YNL170W NELP2 YPL017C YPL017C NELP2 YTA7 YGR270W NFAB1 AOR1 YBR231C NFAB1 ARP1 YHR129C YFAB1 ARP6 YLR085C NFAB1 ASE1 YOR058C NFAB1 BEM1 YBR200W NFAB1 BFA1 YJR053W NFAB1 BIK1 YCL029C YFAB1 BIM1 YER016W YFAB1 BUB1 YGR188C NFAB1 BUB2 YMR055C NFAB1 BUB3 YOR026W NFAB1 CHL4 YDR254W NFAB1 CSM3 YMR048W NFAB1 CTF19 YPL018W NFAB1 CTF3 YLR381W NFAB1 CTF8 YHR191C NFAB1 DCC1 YCL016C YFAB1 DYN1 YKR054C YFAB1 ELP2 YGR200C NFAB1 GIM3 YNL153C YFAB1 GIM4 YEL003W YFAB1 GIM5 YML094W YFAB1 IES2 YNL215W NFAB1 IML3 YBR107C NFAB1 INP52 YNL106C NFAB1 JNM1 YMR294W YFAB1 KEM1 YGL173C YFAB1 KIP3 YGL216W NFAB1 MAD1 YGL086W NFAB1 MAD2 YJL030W NFAB1 MAD3 YJL013C NFAB1 MCK1 YNL307C YFAB1 MCM21 YDR318W NFAB1 MCM22 YJR135C NFAB1 MRC1 YCL060C YFAB1 NBP2 YDR162C NFAB1 NUM1 YDR150W YFAB1 PAC1 YOR269W NFAB1 PAC11 YDR488C YFAB1 PHO23 YNL097C NFAB1 PPZ1 YML016C NFAB1 RAD54 YGL163C NFAB1 RTT103 YDR289C NFAB1 SAP30 YMR263W NFAB1 SLK19 YOR195W N

Page 129: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

FAB1 SMI1 YGR229C NFAB1 VAC14 YLR386W NFAB1 VID22 YLR373C NFAB1 RXT2 RXT2 NFAB1 YDR149C YDR149C YFAB1 YGL211W YGL211W NFAB1 YGL217C YGL217C NFAB1 YML095C-A YML095C-A NFAB1 YNL170W YNL170W NFAB1 YPL017C YPL017C NFAB1 YTA7 YGR270W NGIM3 AOR1 YBR231C YGIM3 ARP1 YHR129C NGIM3 ARP6 YLR085C YGIM3 ASE1 YOR058C NGIM3 BEM1 YBR200W YGIM3 BFA1 YJR053W NGIM3 BIK1 YCL029C YGIM3 BIM1 YER016W YGIM3 BUB1 YGR188C YGIM3 BUB2 YMR055C NGIM3 BUB3 YOR026W NGIM3 CHL4 YDR254W NGIM3 CSM3 YMR048W NGIM3 CTF19 YPL018W YGIM3 CTF3 YLR381W NGIM3 CTF8 YHR191C YGIM3 DCC1 YCL016C YGIM3 DYN1 YKR054C NGIM3 ELP2 YGR200C NGIM3 FAB1 YFR019W YGIM3 GIM4 YEL003W NGIM3 GIM5 YML094W NGIM3 IES2 YNL215W NGIM3 IML3 YBR107C NGIM3 INP52 YNL106C YGIM3 JNM1 YMR294W NGIM3 KEM1 YGL173C YGIM3 KIP3 YGL216W NGIM3 MAD1 YGL086W NGIM3 MAD2 YJL030W NGIM3 MAD3 YJL013C NGIM3 MCK1 YNL307C NGIM3 MCM21 YDR318W NGIM3 MCM22 YJR135C NGIM3 MRC1 YCL060C NGIM3 NBP2 YDR162C NGIM3 NUM1 YDR150W YGIM3 PAC1 YOR269W NGIM3 PAC11 YDR488C NGIM3 PHO23 YNL097C NGIM3 PPZ1 YML016C NGIM3 RAD54 YGL163C NGIM3 RTT103 YDR289C NGIM3 SAP30 YMR263W NGIM3 SLK19 YOR195W NGIM3 SMI1 YGR229C NGIM3 VAC14 YLR386W NGIM3 VID22 YLR373C NGIM3 RXT2 RXT2 NGIM3 YDR149C YDR149C NGIM3 YGL211W YGL211W NGIM3 YGL217C YGL217C NGIM3 YML095C-A YML095C-A NGIM3 YNL170W YNL170W YGIM3 YPL017C YPL017C N

Page 130: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

GIM3 YTA7 YGR270W NGIM4 AOR1 YBR231C YGIM4 ARP1 YHR129C NGIM4 ARP6 YLR085C YGIM4 ASE1 YOR058C NGIM4 BEM1 YBR200W NGIM4 BFA1 YJR053W NGIM4 BIK1 YCL029C YGIM4 BIM1 YER016W YGIM4 BUB1 YGR188C YGIM4 BUB2 YMR055C YGIM4 BUB3 YOR026W YGIM4 CHL4 YDR254W NGIM4 CSM3 YMR048W NGIM4 CTF19 YPL018W NGIM4 CTF3 YLR381W NGIM4 CTF8 YHR191C NGIM4 DCC1 YCL016C NGIM4 DYN1 YKR054C NGIM4 ELP2 YGR200C NGIM4 FAB1 YFR019W YGIM4 GIM3 YNL153C NGIM4 GIM5 YML094W NGIM4 IES2 YNL215W NGIM4 IML3 YBR107C NGIM4 INP52 YNL106C YGIM4 JNM1 YMR294W NGIM4 KEM1 YGL173C NGIM4 KIP3 YGL216W NGIM4 MAD1 YGL086W YGIM4 MAD2 YJL030W YGIM4 MAD3 YJL013C NGIM4 MCK1 YNL307C NGIM4 MCM21 YDR318W NGIM4 MCM22 YJR135C NGIM4 MRC1 YCL060C NGIM4 NBP2 YDR162C NGIM4 NUM1 YDR150W NGIM4 PAC1 YOR269W NGIM4 PAC11 YDR488C NGIM4 PHO23 YNL097C NGIM4 PPZ1 YML016C NGIM4 RAD54 YGL163C NGIM4 RTT103 YDR289C NGIM4 SAP30 YMR263W NGIM4 SLK19 YOR195W NGIM4 SMI1 YGR229C NGIM4 VAC14 YLR386W NGIM4 VID22 YLR373C NGIM4 RXT2 RXT2 NGIM4 YDR149C YDR149C NGIM4 YGL211W YGL211W NGIM4 YGL217C YGL217C NGIM4 YML095C-A YML095C-A NGIM4 YNL170W YNL170W NGIM4 YPL017C YPL017C NGIM4 YTA7 YGR270W NGIM5 AOR1 YBR231C YGIM5 ARP1 YHR129C YGIM5 ARP6 YLR085C YGIM5 ASE1 YOR058C YGIM5 BEM1 YBR200W YGIM5 BFA1 YJR053W YGIM5 BIK1 YCL029C YGIM5 BIM1 YER016W YGIM5 BUB1 YGR188C Y

Page 131: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

GIM5 BUB2 YMR055C YGIM5 BUB3 YOR026W YGIM5 CHL4 YDR254W YGIM5 CSM3 YMR048W NGIM5 CTF19 YPL018W YGIM5 CTF3 YLR381W NGIM5 CTF8 YHR191C YGIM5 DCC1 YCL016C YGIM5 DYN1 YKR054C YGIM5 ELP2 YGR200C NGIM5 FAB1 YFR019W YGIM5 GIM3 YNL153C NGIM5 GIM4 YEL003W NGIM5 IES2 YNL215W NGIM5 IML3 YBR107C NGIM5 INP52 YNL106C NGIM5 JNM1 YMR294W YGIM5 KEM1 YGL173C YGIM5 KIP3 YGL216W NGIM5 MAD1 YGL086W YGIM5 MAD2 YJL030W YGIM5 MAD3 YJL013C NGIM5 MCK1 YNL307C NGIM5 MCM21 YDR318W YGIM5 MCM22 YJR135C NGIM5 MRC1 YCL060C NGIM5 NBP2 YDR162C YGIM5 NUM1 YDR150W YGIM5 PAC1 YOR269W NGIM5 PAC11 YDR488C YGIM5 PHO23 YNL097C NGIM5 PPZ1 YML016C NGIM5 RAD54 YGL163C NGIM5 RTT103 YDR289C NGIM5 SAP30 YMR263W NGIM5 SLK19 YOR195W NGIM5 SMI1 YGR229C NGIM5 VAC14 YLR386W YGIM5 VID22 YLR373C NGIM5 RXT2 RXT2 NGIM5 YDR149C YDR149C YGIM5 YGL211W YGL211W NGIM5 YGL217C YGL217C NGIM5 YML095C-A YML095C-A YGIM5 YNL170W YNL170W NGIM5 YPL017C YPL017C NGIM5 YTA7 YGR270W NIES2 AOR1 YBR231C NIES2 ARP1 YHR129C NIES2 ARP6 YLR085C NIES2 ASE1 YOR058C NIES2 BEM1 YBR200W NIES2 BFA1 YJR053W NIES2 BIK1 YCL029C NIES2 BIM1 YER016W YIES2 BUB1 YGR188C NIES2 BUB2 YMR055C NIES2 BUB3 YOR026W YIES2 CHL4 YDR254W NIES2 CSM3 YMR048W NIES2 CTF19 YPL018W NIES2 CTF3 YLR381W YIES2 CTF8 YHR191C NIES2 DCC1 YCL016C NIES2 DYN1 YKR054C NIES2 ELP2 YGR200C N

Page 132: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

IES2 FAB1 YFR019W NIES2 GIM3 YNL153C YIES2 GIM4 YEL003W NIES2 GIM5 YML094W NIES2 IML3 YBR107C NIES2 INP52 YNL106C NIES2 JNM1 YMR294W NIES2 KEM1 YGL173C NIES2 KIP3 YGL216W NIES2 MAD1 YGL086W NIES2 MAD2 YJL030W NIES2 MAD3 YJL013C NIES2 MCK1 YNL307C NIES2 MCM21 YDR318W NIES2 MCM22 YJR135C NIES2 MRC1 YCL060C NIES2 NBP2 YDR162C NIES2 NUM1 YDR150W NIES2 PAC1 YOR269W NIES2 PAC11 YDR488C NIES2 PHO23 YNL097C NIES2 PPZ1 YML016C NIES2 RAD54 YGL163C NIES2 RTT103 YDR289C NIES2 SAP30 YMR263W NIES2 SLK19 YOR195W NIES2 SMI1 YGR229C NIES2 VAC14 YLR386W YIES2 VID22 YLR373C NIES2 RXT2 RXT2 NIES2 YDR149C YDR149C NIES2 YGL211W YGL211W NIES2 YGL217C YGL217C NIES2 YML095C-A YML095C-A NIES2 YNL170W YNL170W NIES2 YPL017C YPL017C NIES2 YTA7 YGR270W NIML3 AOR1 YBR231C NIML3 ARP1 YHR129C NIML3 ARP6 YLR085C NIML3 ASE1 YOR058C NIML3 BEM1 YBR200W NIML3 BFA1 YJR053W NIML3 BIK1 YCL029C NIML3 BIM1 YER016W YIML3 BUB1 YGR188C YIML3 BUB2 YMR055C NIML3 BUB3 YOR026W YIML3 CHL4 YDR254W NIML3 CSM3 YMR048W NIML3 CTF19 YPL018W NIML3 CTF3 YLR381W NIML3 CTF8 YHR191C NIML3 DCC1 YCL016C NIML3 DYN1 YKR054C NIML3 ELP2 YGR200C NIML3 FAB1 YFR019W NIML3 GIM3 YNL153C NIML3 GIM4 YEL003W NIML3 GIM5 YML094W NIML3 IES2 YNL215W NIML3 INP52 YNL106C NIML3 JNM1 YMR294W NIML3 KEM1 YGL173C NIML3 KIP3 YGL216W NIML3 MAD1 YGL086W N

Page 133: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

IML3 MAD2 YJL030W NIML3 MAD3 YJL013C NIML3 MCK1 YNL307C NIML3 MCM21 YDR318W NIML3 MCM22 YJR135C NIML3 MRC1 YCL060C NIML3 NBP2 YDR162C NIML3 NUM1 YDR150W NIML3 PAC1 YOR269W NIML3 PAC11 YDR488C NIML3 PHO23 YNL097C NIML3 PPZ1 YML016C NIML3 RAD54 YGL163C NIML3 RTT103 YDR289C NIML3 SAP30 YMR263W NIML3 SLK19 YOR195W NIML3 SMI1 YGR229C NIML3 VAC14 YLR386W NIML3 VID22 YLR373C NIML3 RXT2 RXT2 YIML3 YDR149C YDR149C NIML3 YGL211W YGL211W NIML3 YGL217C YGL217C NIML3 YML095C-A YML095C-A YIML3 YNL170W YNL170W NIML3 YPL017C YPL017C NIML3 YTA7 YGR270W NINP52 AOR1 YBR231C NINP52 ARP1 YHR129C NINP52 ARP6 YLR085C NINP52 ASE1 YOR058C NINP52 BEM1 YBR200W NINP52 BFA1 YJR053W NINP52 BIK1 YCL029C YINP52 BIM1 YER016W YINP52 BUB1 YGR188C YINP52 BUB2 YMR055C NINP52 BUB3 YOR026W YINP52 CHL4 YDR254W NINP52 CSM3 YMR048W NINP52 CTF19 YPL018W NINP52 CTF3 YLR381W NINP52 CTF8 YHR191C NINP52 DCC1 YCL016C YINP52 DYN1 YKR054C NINP52 ELP2 YGR200C NINP52 FAB1 YFR019W NINP52 GIM3 YNL153C YINP52 GIM4 YEL003W YINP52 GIM5 YML094W YINP52 IES2 YNL215W NINP52 IML3 YBR107C NINP52 JNM1 YMR294W NINP52 KEM1 YGL173C YINP52 KIP3 YGL216W NINP52 MAD1 YGL086W YINP52 MAD2 YJL030W NINP52 MAD3 YJL013C NINP52 MCK1 YNL307C NINP52 MCM21 YDR318W NINP52 MCM22 YJR135C NINP52 MRC1 YCL060C YINP52 NBP2 YDR162C NINP52 NUM1 YDR150W NINP52 PAC1 YOR269W NINP52 PAC11 YDR488C N

Page 134: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

INP52 PHO23 YNL097C YINP52 PPZ1 YML016C NINP52 RAD54 YGL163C NINP52 RTT103 YDR289C YINP52 SAP30 YMR263W YINP52 SLK19 YOR195W NINP52 SMI1 YGR229C NINP52 VAC14 YLR386W NINP52 VID22 YLR373C YINP52 RXT2 RXT2 YINP52 YDR149C YDR149C NINP52 YGL211W YGL211W NINP52 YGL217C YGL217C NINP52 YML095C-A YML095C-A NINP52 YNL170W YNL170W NINP52 YPL017C YPL017C NINP52 YTA7 YGR270W NJNM1 AOR1 YBR231C NJNM1 ARP1 YHR129C NJNM1 ARP6 YLR085C NJNM1 ASE1 YOR058C YJNM1 BEM1 YBR200W NJNM1 BFA1 YJR053W NJNM1 BIK1 YCL029C NJNM1 BIM1 YER016W YJNM1 BUB1 YGR188C NJNM1 BUB2 YMR055C NJNM1 BUB3 YOR026W NJNM1 CHL4 YDR254W NJNM1 CSM3 YMR048W NJNM1 CTF19 YPL018W NJNM1 CTF3 YLR381W NJNM1 CTF8 YHR191C NJNM1 DCC1 YCL016C NJNM1 DYN1 YKR054C NJNM1 ELP2 YGR200C NJNM1 FAB1 YFR019W YJNM1 GIM3 YNL153C YJNM1 GIM4 YEL003W YJNM1 GIM5 YML094W YJNM1 IES2 YNL215W NJNM1 IML3 YBR107C NJNM1 INP52 YNL106C NJNM1 KEM1 YGL173C NJNM1 KIP3 YGL216W YJNM1 MAD1 YGL086W NJNM1 MAD2 YJL030W NJNM1 MAD3 YJL013C NJNM1 MCK1 YNL307C NJNM1 MCM21 YDR318W NJNM1 MCM22 YJR135C NJNM1 MRC1 YCL060C NJNM1 NBP2 YDR162C NJNM1 NUM1 YDR150W NJNM1 PAC1 YOR269W NJNM1 PAC11 YDR488C NJNM1 PHO23 YNL097C NJNM1 PPZ1 YML016C NJNM1 RAD54 YGL163C NJNM1 RTT103 YDR289C NJNM1 SAP30 YMR263W NJNM1 SLK19 YOR195W NJNM1 SMI1 YGR229C NJNM1 VAC14 YLR386W NJNM1 VID22 YLR373C NJNM1 RXT2 RXT2 N

Page 135: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

JNM1 YDR149C YDR149C NJNM1 YGL211W YGL211W NJNM1 YGL217C YGL217C YJNM1 YML095C-A YML095C-A NJNM1 YNL170W YNL170W NJNM1 YPL017C YPL017C NJNM1 YTA7 YGR270W NKEM1 AOR1 YBR231C NKEM1 ARP1 YHR129C NKEM1 ARP6 YLR085C NKEM1 ASE1 YOR058C NKEM1 BEM1 YBR200W YKEM1 BFA1 YJR053W NKEM1 BIK1 YCL029C NKEM1 BIM1 YER016W YKEM1 BUB1 YGR188C YKEM1 BUB2 YMR055C NKEM1 BUB3 YOR026W YKEM1 CHL4 YDR254W NKEM1 CSM3 YMR048W NKEM1 CTF19 YPL018W NKEM1 CTF3 YLR381W YKEM1 CTF8 YHR191C NKEM1 DCC1 YCL016C NKEM1 DYN1 YKR054C NKEM1 ELP2 YGR200C YKEM1 FAB1 YFR019W YKEM1 GIM3 YNL153C YKEM1 GIM4 YEL003W NKEM1 GIM5 YML094W YKEM1 IES2 YNL215W YKEM1 IML3 YBR107C NKEM1 INP52 YNL106C NKEM1 JNM1 YMR294W NKEM1 KIP3 YGL216W NKEM1 MAD1 YGL086W NKEM1 MAD2 YJL030W NKEM1 MAD3 YJL013C NKEM1 MCK1 YNL307C NKEM1 MCM21 YDR318W NKEM1 MCM22 YJR135C NKEM1 MRC1 YCL060C NKEM1 NBP2 YDR162C YKEM1 NUM1 YDR150W NKEM1 PAC1 YOR269W NKEM1 PAC11 YDR488C NKEM1 PHO23 YNL097C YKEM1 PPZ1 YML016C NKEM1 RAD54 YGL163C YKEM1 RTT103 YDR289C NKEM1 SAP30 YMR263W YKEM1 SLK19 YOR195W NKEM1 SMI1 YGR229C NKEM1 VAC14 YLR386W NKEM1 VID22 YLR373C YKEM1 RXT2 RXT2 NKEM1 YDR149C YDR149C NKEM1 YGL211W YGL211W YKEM1 YGL217C YGL217C NKEM1 YML095C-A YML095C-A NKEM1 YNL170W YNL170W NKEM1 YPL017C YPL017C NKEM1 YTA7 YGR270W NKIP3 AOR1 YBR231C NKIP3 ARP1 YHR129C YKIP3 ARP6 YLR085C N

Page 136: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

KIP3 ASE1 YOR058C NKIP3 BEM1 YBR200W NKIP3 BFA1 YJR053W NKIP3 BIK1 YCL029C NKIP3 BIM1 YER016W YKIP3 BUB1 YGR188C NKIP3 BUB2 YMR055C NKIP3 BUB3 YOR026W YKIP3 CHL4 YDR254W NKIP3 CSM3 YMR048W NKIP3 CTF19 YPL018W NKIP3 CTF3 YLR381W NKIP3 CTF8 YHR191C NKIP3 DCC1 YCL016C NKIP3 DYN1 YKR054C YKIP3 ELP2 YGR200C NKIP3 FAB1 YFR019W NKIP3 GIM3 YNL153C NKIP3 GIM4 YEL003W NKIP3 GIM5 YML094W NKIP3 IES2 YNL215W NKIP3 IML3 YBR107C NKIP3 INP52 YNL106C NKIP3 JNM1 YMR294W YKIP3 KEM1 YGL173C NKIP3 MAD1 YGL086W NKIP3 MAD2 YJL030W NKIP3 MAD3 YJL013C NKIP3 MCK1 YNL307C NKIP3 MCM21 YDR318W NKIP3 MCM22 YJR135C NKIP3 MRC1 YCL060C NKIP3 NBP2 YDR162C YKIP3 NUM1 YDR150W YKIP3 PAC1 YOR269W YKIP3 PAC11 YDR488C YKIP3 PHO23 YNL097C NKIP3 PPZ1 YML016C NKIP3 RAD54 YGL163C NKIP3 RTT103 YDR289C NKIP3 SAP30 YMR263W NKIP3 SLK19 YOR195W NKIP3 SMI1 YGR229C NKIP3 VAC14 YLR386W NKIP3 VID22 YLR373C NKIP3 RXT2 RXT2 NKIP3 YDR149C YDR149C YKIP3 YGL211W YGL211W YKIP3 YGL217C YGL217C YKIP3 YML095C-A YML095C-A NKIP3 YNL170W YNL170W NKIP3 YPL017C YPL017C NKIP3 YTA7 YGR270W NMAD1 AOR1 YBR231C NMAD1 ARP1 YHR129C NMAD1 ARP6 YLR085C NMAD1 ASE1 YOR058C NMAD1 BEM1 YBR200W NMAD1 BFA1 YJR053W NMAD1 BIK1 YCL029C NMAD1 BIM1 YER016W YMAD1 BUB1 YGR188C NMAD1 BUB2 YMR055C NMAD1 BUB3 YOR026W NMAD1 CHL4 YDR254W NMAD1 CSM3 YMR048W N

Page 137: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

MAD1 CTF19 YPL018W YMAD1 CTF3 YLR381W NMAD1 CTF8 YHR191C NMAD1 DCC1 YCL016C NMAD1 DYN1 YKR054C NMAD1 ELP2 YGR200C NMAD1 FAB1 YFR019W NMAD1 GIM3 YNL153C NMAD1 GIM4 YEL003W YMAD1 GIM5 YML094W YMAD1 IES2 YNL215W NMAD1 IML3 YBR107C NMAD1 INP52 YNL106C YMAD1 JNM1 YMR294W NMAD1 KEM1 YGL173C NMAD1 KIP3 YGL216W NMAD1 MAD2 YJL030W NMAD1 MAD3 YJL013C NMAD1 MCK1 YNL307C NMAD1 MCM21 YDR318W YMAD1 MCM22 YJR135C NMAD1 MRC1 YCL060C NMAD1 NBP2 YDR162C NMAD1 NUM1 YDR150W NMAD1 PAC1 YOR269W NMAD1 PAC11 YDR488C NMAD1 PHO23 YNL097C NMAD1 PPZ1 YML016C NMAD1 RAD54 YGL163C NMAD1 RTT103 YDR289C NMAD1 SAP30 YMR263W NMAD1 SLK19 YOR195W NMAD1 SMI1 YGR229C NMAD1 VAC14 YLR386W NMAD1 VID22 YLR373C NMAD1 RXT2 RXT2 NMAD1 YDR149C YDR149C NMAD1 YGL211W YGL211W NMAD1 YGL217C YGL217C NMAD1 YML095C-A YML095C-A NMAD1 YNL170W YNL170W NMAD1 YPL017C YPL017C NMAD1 YTA7 YGR270W NMAD2 AOR1 YBR231C NMAD2 ARP1 YHR129C NMAD2 ARP6 YLR085C NMAD2 ASE1 YOR058C NMAD2 BEM1 YBR200W NMAD2 BFA1 YJR053W NMAD2 BIK1 YCL029C NMAD2 BIM1 YER016W YMAD2 BUB1 YGR188C NMAD2 BUB2 YMR055C NMAD2 BUB3 YOR026W NMAD2 CHL4 YDR254W NMAD2 CSM3 YMR048W NMAD2 CTF19 YPL018W YMAD2 CTF3 YLR381W NMAD2 CTF8 YHR191C NMAD2 DCC1 YCL016C NMAD2 DYN1 YKR054C NMAD2 ELP2 YGR200C NMAD2 FAB1 YFR019W NMAD2 GIM3 YNL153C NMAD2 GIM4 YEL003W YMAD2 GIM5 YML094W N

Page 138: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

MAD2 IES2 YNL215W NMAD2 IML3 YBR107C NMAD2 INP52 YNL106C NMAD2 JNM1 YMR294W NMAD2 KEM1 YGL173C NMAD2 KIP3 YGL216W NMAD2 MAD1 YGL086W NMAD2 MAD3 YJL013C YMAD2 MCK1 YNL307C NMAD2 MCM21 YDR318W YMAD2 MCM22 YJR135C NMAD2 MRC1 YCL060C NMAD2 NBP2 YDR162C NMAD2 NUM1 YDR150W NMAD2 PAC1 YOR269W NMAD2 PAC11 YDR488C NMAD2 PHO23 YNL097C NMAD2 PPZ1 YML016C NMAD2 RAD54 YGL163C NMAD2 RTT103 YDR289C NMAD2 SAP30 YMR263W NMAD2 SLK19 YOR195W NMAD2 SMI1 YGR229C NMAD2 VAC14 YLR386W NMAD2 VID22 YLR373C NMAD2 RXT2 RXT2 NMAD2 YDR149C YDR149C NMAD2 YGL211W YGL211W NMAD2 YGL217C YGL217C NMAD2 YML095C-A YML095C-A NMAD2 YNL170W YNL170W NMAD2 YPL017C YPL017C NMAD2 YTA7 YGR270W NMAD3 AOR1 YBR231C NMAD3 ARP1 YHR129C NMAD3 ARP6 YLR085C NMAD3 ASE1 YOR058C NMAD3 BEM1 YBR200W NMAD3 BFA1 YJR053W NMAD3 BIK1 YCL029C NMAD3 BIM1 YER016W YMAD3 BUB1 YGR188C NMAD3 BUB2 YMR055C NMAD3 BUB3 YOR026W NMAD3 CHL4 YDR254W NMAD3 CSM3 YMR048W NMAD3 CTF19 YPL018W NMAD3 CTF3 YLR381W NMAD3 CTF8 YHR191C NMAD3 DCC1 YCL016C NMAD3 DYN1 YKR054C NMAD3 ELP2 YGR200C NMAD3 FAB1 YFR019W NMAD3 GIM3 YNL153C NMAD3 GIM4 YEL003W NMAD3 GIM5 YML094W NMAD3 IES2 YNL215W NMAD3 IML3 YBR107C NMAD3 INP52 YNL106C NMAD3 JNM1 YMR294W NMAD3 KEM1 YGL173C NMAD3 KIP3 YGL216W NMAD3 MAD1 YGL086W NMAD3 MAD2 YJL030W YMAD3 MCK1 YNL307C NMAD3 MCM21 YDR318W N

Page 139: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

MAD3 MCM22 YJR135C NMAD3 MRC1 YCL060C NMAD3 NBP2 YDR162C NMAD3 NUM1 YDR150W NMAD3 PAC1 YOR269W NMAD3 PAC11 YDR488C NMAD3 PHO23 YNL097C NMAD3 PPZ1 YML016C NMAD3 RAD54 YGL163C NMAD3 RTT103 YDR289C NMAD3 SAP30 YMR263W NMAD3 SLK19 YOR195W NMAD3 SMI1 YGR229C NMAD3 VAC14 YLR386W NMAD3 VID22 YLR373C NMAD3 RXT2 RXT2 NMAD3 YDR149C YDR149C NMAD3 YGL211W YGL211W NMAD3 YGL217C YGL217C NMAD3 YML095C-A YML095C-A NMAD3 YNL170W YNL170W NMAD3 YPL017C YPL017C NMAD3 YTA7 YGR270W NMCK1 AOR1 YBR231C NMCK1 ARP1 YHR129C NMCK1 ARP6 YLR085C NMCK1 ASE1 YOR058C NMCK1 BEM1 YBR200W NMCK1 BFA1 YJR053W NMCK1 BIK1 YCL029C NMCK1 BIM1 YER016W YMCK1 BUB1 YGR188C NMCK1 BUB2 YMR055C NMCK1 BUB3 YOR026W YMCK1 CHL4 YDR254W NMCK1 CSM3 YMR048W NMCK1 CTF19 YPL018W NMCK1 CTF3 YLR381W NMCK1 CTF8 YHR191C YMCK1 DCC1 YCL016C NMCK1 DYN1 YKR054C NMCK1 ELP2 YGR200C NMCK1 FAB1 YFR019W YMCK1 GIM3 YNL153C NMCK1 GIM4 YEL003W NMCK1 GIM5 YML094W NMCK1 IES2 YNL215W NMCK1 IML3 YBR107C NMCK1 INP52 YNL106C NMCK1 JNM1 YMR294W NMCK1 KEM1 YGL173C NMCK1 KIP3 YGL216W NMCK1 MAD1 YGL086W NMCK1 MAD2 YJL030W NMCK1 MAD3 YJL013C NMCK1 MCM21 YDR318W NMCK1 MCM22 YJR135C NMCK1 MRC1 YCL060C NMCK1 NBP2 YDR162C YMCK1 NUM1 YDR150W NMCK1 PAC1 YOR269W NMCK1 PAC11 YDR488C NMCK1 PHO23 YNL097C YMCK1 PPZ1 YML016C NMCK1 RAD54 YGL163C NMCK1 RTT103 YDR289C N

Page 140: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

MCK1 SAP30 YMR263W NMCK1 SLK19 YOR195W NMCK1 SMI1 YGR229C NMCK1 VAC14 YLR386W NMCK1 VID22 YLR373C NMCK1 RXT2 RXT2 NMCK1 YDR149C YDR149C NMCK1 YGL211W YGL211W NMCK1 YGL217C YGL217C NMCK1 YML095C-A YML095C-A NMCK1 YNL170W YNL170W NMCK1 YPL017C YPL017C NMCK1 YTA7 YGR270W NMCM21 AOR1 YBR231C NMCM21 ARP1 YHR129C NMCM21 ARP6 YLR085C NMCM21 ASE1 YOR058C NMCM21 BEM1 YBR200W NMCM21 BFA1 YJR053W NMCM21 BIK1 YCL029C NMCM21 BIM1 YER016W YMCM21 BUB1 YGR188C YMCM21 BUB2 YMR055C NMCM21 BUB3 YOR026W YMCM21 CHL4 YDR254W NMCM21 CSM3 YMR048W NMCM21 CTF19 YPL018W NMCM21 CTF3 YLR381W NMCM21 CTF8 YHR191C NMCM21 DCC1 YCL016C NMCM21 DYN1 YKR054C NMCM21 ELP2 YGR200C NMCM21 FAB1 YFR019W NMCM21 GIM3 YNL153C YMCM21 GIM4 YEL003W NMCM21 GIM5 YML094W YMCM21 IES2 YNL215W NMCM21 IML3 YBR107C NMCM21 INP52 YNL106C NMCM21 JNM1 YMR294W NMCM21 KEM1 YGL173C NMCM21 KIP3 YGL216W NMCM21 MAD1 YGL086W YMCM21 MAD2 YJL030W YMCM21 MAD3 YJL013C NMCM21 MCK1 YNL307C NMCM21 MCM22 YJR135C NMCM21 MRC1 YCL060C NMCM21 NBP2 YDR162C NMCM21 NUM1 YDR150W NMCM21 PAC1 YOR269W NMCM21 PAC11 YDR488C NMCM21 PHO23 YNL097C NMCM21 PPZ1 YML016C NMCM21 RAD54 YGL163C NMCM21 RTT103 YDR289C NMCM21 SAP30 YMR263W NMCM21 SLK19 YOR195W NMCM21 SMI1 YGR229C NMCM21 VAC14 YLR386W NMCM21 VID22 YLR373C NMCM21 RXT2 RXT2 NMCM21 YDR149C YDR149C NMCM21 YGL211W YGL211W NMCM21 YGL217C YGL217C NMCM21 YML095C-A YML095C-A Y

Page 141: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

MCM21 YNL170W YNL170W NMCM21 YPL017C YPL017C NMCM21 YTA7 YGR270W NMCM22 AOR1 YBR231C NMCM22 ARP1 YHR129C NMCM22 ARP6 YLR085C NMCM22 ASE1 YOR058C NMCM22 BEM1 YBR200W NMCM22 BFA1 YJR053W NMCM22 BIK1 YCL029C NMCM22 BIM1 YER016W YMCM22 BUB1 YGR188C YMCM22 BUB2 YMR055C NMCM22 BUB3 YOR026W YMCM22 CHL4 YDR254W NMCM22 CSM3 YMR048W NMCM22 CTF19 YPL018W NMCM22 CTF3 YLR381W NMCM22 CTF8 YHR191C NMCM22 DCC1 YCL016C NMCM22 DYN1 YKR054C NMCM22 ELP2 YGR200C NMCM22 FAB1 YFR019W NMCM22 GIM3 YNL153C NMCM22 GIM4 YEL003W NMCM22 GIM5 YML094W NMCM22 IES2 YNL215W NMCM22 IML3 YBR107C NMCM22 INP52 YNL106C NMCM22 JNM1 YMR294W NMCM22 KEM1 YGL173C NMCM22 KIP3 YGL216W NMCM22 MAD1 YGL086W NMCM22 MAD2 YJL030W NMCM22 MAD3 YJL013C NMCM22 MCK1 YNL307C NMCM22 MCM21 YDR318W NMCM22 MRC1 YCL060C NMCM22 NBP2 YDR162C NMCM22 NUM1 YDR150W NMCM22 PAC1 YOR269W NMCM22 PAC11 YDR488C NMCM22 PHO23 YNL097C NMCM22 PPZ1 YML016C NMCM22 RAD54 YGL163C NMCM22 RTT103 YDR289C NMCM22 SAP30 YMR263W NMCM22 SLK19 YOR195W NMCM22 SMI1 YGR229C NMCM22 VAC14 YLR386W NMCM22 VID22 YLR373C NMCM22 RXT2 RXT2 NMCM22 YDR149C YDR149C NMCM22 YGL211W YGL211W NMCM22 YGL217C YGL217C NMCM22 YML095C-A YML095C-A NMCM22 YNL170W YNL170W NMCM22 YPL017C YPL017C NMCM22 YTA7 YGR270W NMRC1 AOR1 YBR231C NMRC1 ARP1 YHR129C NMRC1 ARP6 YLR085C NMRC1 ASE1 YOR058C NMRC1 BEM1 YBR200W NMRC1 BFA1 YJR053W NMRC1 BIK1 YCL029C N

Page 142: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

MRC1 BIM1 YER016W YMRC1 BUB1 YGR188C NMRC1 BUB2 YMR055C NMRC1 BUB3 YOR026W NMRC1 CHL4 YDR254W NMRC1 CSM3 YMR048W YMRC1 CTF19 YPL018W NMRC1 CTF3 YLR381W NMRC1 CTF8 YHR191C YMRC1 DCC1 YCL016C YMRC1 DYN1 YKR054C NMRC1 ELP2 YGR200C NMRC1 FAB1 YFR019W NMRC1 GIM3 YNL153C NMRC1 GIM4 YEL003W NMRC1 GIM5 YML094W NMRC1 IES2 YNL215W NMRC1 IML3 YBR107C NMRC1 INP52 YNL106C YMRC1 JNM1 YMR294W NMRC1 KEM1 YGL173C NMRC1 KIP3 YGL216W NMRC1 MAD1 YGL086W NMRC1 MAD2 YJL030W NMRC1 MAD3 YJL013C NMRC1 MCK1 YNL307C NMRC1 MCM21 YDR318W NMRC1 MCM22 YJR135C NMRC1 NBP2 YDR162C NMRC1 NUM1 YDR150W NMRC1 PAC1 YOR269W NMRC1 PAC11 YDR488C NMRC1 PHO23 YNL097C NMRC1 PPZ1 YML016C NMRC1 RAD54 YGL163C NMRC1 RTT103 YDR289C NMRC1 SAP30 YMR263W NMRC1 SLK19 YOR195W NMRC1 SMI1 YGR229C NMRC1 VAC14 YLR386W NMRC1 VID22 YLR373C NMRC1 RXT2 RXT2 NMRC1 YDR149C YDR149C NMRC1 YGL211W YGL211W NMRC1 YGL217C YGL217C NMRC1 YML095C-A YML095C-A NMRC1 YNL170W YNL170W NMRC1 YPL017C YPL017C NMRC1 YTA7 YGR270W NNBP2 AOR1 YBR231C NNBP2 ARP1 YHR129C NNBP2 ARP6 YLR085C NNBP2 ASE1 YOR058C NNBP2 BEM1 YBR200W NNBP2 BFA1 YJR053W NNBP2 BIK1 YCL029C NNBP2 BIM1 YER016W YNBP2 BUB1 YGR188C NNBP2 BUB2 YMR055C NNBP2 BUB3 YOR026W NNBP2 CHL4 YDR254W NNBP2 CSM3 YMR048W NNBP2 CTF19 YPL018W NNBP2 CTF3 YLR381W NNBP2 CTF8 YHR191C NNBP2 DCC1 YCL016C N

Page 143: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

NBP2 DYN1 YKR054C NNBP2 ELP2 YGR200C NNBP2 FAB1 YFR019W NNBP2 GIM3 YNL153C NNBP2 GIM4 YEL003W NNBP2 GIM5 YML094W NNBP2 IES2 YNL215W NNBP2 IML3 YBR107C NNBP2 INP52 YNL106C NNBP2 JNM1 YMR294W NNBP2 KEM1 YGL173C NNBP2 KIP3 YGL216W YNBP2 MAD1 YGL086W NNBP2 MAD2 YJL030W NNBP2 MAD3 YJL013C NNBP2 MCK1 YNL307C NNBP2 MCM21 YDR318W NNBP2 MCM22 YJR135C NNBP2 MRC1 YCL060C NNBP2 NUM1 YDR150W NNBP2 PAC1 YOR269W NNBP2 PAC11 YDR488C NNBP2 PHO23 YNL097C NNBP2 PPZ1 YML016C NNBP2 RAD54 YGL163C NNBP2 RTT103 YDR289C NNBP2 SAP30 YMR263W NNBP2 SLK19 YOR195W NNBP2 SMI1 YGR229C NNBP2 VAC14 YLR386W NNBP2 VID22 YLR373C NNBP2 RXT2 RXT2 NNBP2 YDR149C YDR149C NNBP2 YGL211W YGL211W YNBP2 YGL217C YGL217C YNBP2 YML095C-A YML095C-A NNBP2 YNL170W YNL170W NNBP2 YPL017C YPL017C NNBP2 YTA7 YGR270W NNUM1 AOR1 YBR231C NNUM1 ARP1 YHR129C NNUM1 ARP6 YLR085C NNUM1 ASE1 YOR058C NNUM1 BEM1 YBR200W NNUM1 BFA1 YJR053W YNUM1 BIK1 YCL029C NNUM1 BIM1 YER016W YNUM1 BUB1 YGR188C NNUM1 BUB2 YMR055C NNUM1 BUB3 YOR026W NNUM1 CHL4 YDR254W NNUM1 CSM3 YMR048W NNUM1 CTF19 YPL018W NNUM1 CTF3 YLR381W NNUM1 CTF8 YHR191C NNUM1 DCC1 YCL016C NNUM1 DYN1 YKR054C NNUM1 ELP2 YGR200C NNUM1 FAB1 YFR019W YNUM1 GIM3 YNL153C YNUM1 GIM4 YEL003W YNUM1 GIM5 YML094W YNUM1 IES2 YNL215W NNUM1 IML3 YBR107C NNUM1 INP52 YNL106C NNUM1 JNM1 YMR294W N

Page 144: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

NUM1 KEM1 YGL173C NNUM1 KIP3 YGL216W YNUM1 MAD1 YGL086W NNUM1 MAD2 YJL030W NNUM1 MAD3 YJL013C NNUM1 MCK1 YNL307C NNUM1 MCM21 YDR318W NNUM1 MCM22 YJR135C NNUM1 MRC1 YCL060C NNUM1 NBP2 YDR162C YNUM1 PAC1 YOR269W NNUM1 PAC11 YDR488C NNUM1 PHO23 YNL097C NNUM1 PPZ1 YML016C NNUM1 RAD54 YGL163C NNUM1 RTT103 YDR289C NNUM1 SAP30 YMR263W NNUM1 SLK19 YOR195W NNUM1 SMI1 YGR229C NNUM1 VAC14 YLR386W NNUM1 VID22 YLR373C NNUM1 RXT2 RXT2 NNUM1 YDR149C YDR149C YNUM1 YGL211W YGL211W NNUM1 YGL217C YGL217C NNUM1 YML095C-A YML095C-A NNUM1 YNL170W YNL170W NNUM1 YPL017C YPL017C NNUM1 YTA7 YGR270W NPAC1 AOR1 YBR231C NPAC1 ARP1 YHR129C NPAC1 ARP6 YLR085C NPAC1 ASE1 YOR058C YPAC1 BEM1 YBR200W NPAC1 BFA1 YJR053W NPAC1 BIK1 YCL029C NPAC1 BIM1 YER016W YPAC1 BUB1 YGR188C NPAC1 BUB2 YMR055C NPAC1 BUB3 YOR026W NPAC1 CHL4 YDR254W NPAC1 CSM3 YMR048W NPAC1 CTF19 YPL018W NPAC1 CTF3 YLR381W NPAC1 CTF8 YHR191C NPAC1 DCC1 YCL016C NPAC1 DYN1 YKR054C NPAC1 ELP2 YGR200C NPAC1 FAB1 YFR019W NPAC1 GIM3 YNL153C YPAC1 GIM4 YEL003W NPAC1 GIM5 YML094W YPAC1 IES2 YNL215W NPAC1 IML3 YBR107C NPAC1 INP52 YNL106C NPAC1 JNM1 YMR294W NPAC1 KEM1 YGL173C NPAC1 KIP3 YGL216W NPAC1 MAD1 YGL086W NPAC1 MAD2 YJL030W NPAC1 MAD3 YJL013C NPAC1 MCK1 YNL307C NPAC1 MCM21 YDR318W NPAC1 MCM22 YJR135C NPAC1 MRC1 YCL060C NPAC1 NBP2 YDR162C N

Page 145: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

PAC1 NUM1 YDR150W NPAC1 PAC11 YDR488C NPAC1 PHO23 YNL097C NPAC1 PPZ1 YML016C NPAC1 RAD54 YGL163C NPAC1 RTT103 YDR289C NPAC1 SAP30 YMR263W NPAC1 SLK19 YOR195W NPAC1 SMI1 YGR229C NPAC1 VAC14 YLR386W NPAC1 VID22 YLR373C NPAC1 RXT2 RXT2 NPAC1 YDR149C YDR149C NPAC1 YGL211W YGL211W NPAC1 YGL217C YGL217C YPAC1 YML095C-A YML095C-A YPAC1 YNL170W YNL170W NPAC1 YPL017C YPL017C NPAC1 YTA7 YGR270W NPAC11 AOR1 YBR231C NPAC11 ARP1 YHR129C NPAC11 ARP6 YLR085C NPAC11 ASE1 YOR058C YPAC11 BEM1 YBR200W NPAC11 BFA1 YJR053W NPAC11 BIK1 YCL029C NPAC11 BIM1 YER016W YPAC11 BUB1 YGR188C NPAC11 BUB2 YMR055C NPAC11 BUB3 YOR026W NPAC11 CHL4 YDR254W NPAC11 CSM3 YMR048W NPAC11 CTF19 YPL018W NPAC11 CTF3 YLR381W NPAC11 CTF8 YHR191C NPAC11 DCC1 YCL016C NPAC11 DYN1 YKR054C NPAC11 ELP2 YGR200C NPAC11 FAB1 YFR019W YPAC11 GIM3 YNL153C YPAC11 GIM4 YEL003W NPAC11 GIM5 YML094W YPAC11 IES2 YNL215W NPAC11 IML3 YBR107C NPAC11 INP52 YNL106C NPAC11 JNM1 YMR294W NPAC11 KEM1 YGL173C NPAC11 KIP3 YGL216W YPAC11 MAD1 YGL086W NPAC11 MAD2 YJL030W NPAC11 MAD3 YJL013C NPAC11 MCK1 YNL307C YPAC11 MCM21 YDR318W NPAC11 MCM22 YJR135C NPAC11 MRC1 YCL060C NPAC11 NBP2 YDR162C NPAC11 NUM1 YDR150W NPAC11 PAC1 YOR269W NPAC11 PHO23 YNL097C NPAC11 PPZ1 YML016C NPAC11 RAD54 YGL163C NPAC11 RTT103 YDR289C NPAC11 SAP30 YMR263W NPAC11 SLK19 YOR195W NPAC11 SMI1 YGR229C NPAC11 VAC14 YLR386W N

Page 146: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

PAC11 VID22 YLR373C NPAC11 RXT2 RXT2 NPAC11 YDR149C YDR149C NPAC11 YGL211W YGL211W NPAC11 YGL217C YGL217C YPAC11 YML095C-A YML095C-A NPAC11 YNL170W YNL170W NPAC11 YPL017C YPL017C NPAC11 YTA7 YGR270W NPHO23 AOR1 YBR231C YPHO23 ARP1 YHR129C NPHO23 ARP6 YLR085C YPHO23 ASE1 YOR058C NPHO23 BEM1 YBR200W NPHO23 BFA1 YJR053W NPHO23 BIK1 YCL029C NPHO23 BIM1 YER016W YPHO23 BUB1 YGR188C NPHO23 BUB2 YMR055C NPHO23 BUB3 YOR026W NPHO23 CHL4 YDR254W NPHO23 CSM3 YMR048W NPHO23 CTF19 YPL018W NPHO23 CTF3 YLR381W NPHO23 CTF8 YHR191C NPHO23 DCC1 YCL016C NPHO23 DYN1 YKR054C NPHO23 ELP2 YGR200C NPHO23 FAB1 YFR019W NPHO23 GIM3 YNL153C NPHO23 GIM4 YEL003W NPHO23 GIM5 YML094W NPHO23 IES2 YNL215W YPHO23 IML3 YBR107C NPHO23 INP52 YNL106C YPHO23 JNM1 YMR294W NPHO23 KEM1 YGL173C NPHO23 KIP3 YGL216W NPHO23 MAD1 YGL086W NPHO23 MAD2 YJL030W NPHO23 MAD3 YJL013C NPHO23 MCK1 YNL307C YPHO23 MCM21 YDR318W NPHO23 MCM22 YJR135C NPHO23 MRC1 YCL060C NPHO23 NBP2 YDR162C NPHO23 NUM1 YDR150W NPHO23 PAC1 YOR269W NPHO23 PAC11 YDR488C NPHO23 PPZ1 YML016C NPHO23 RAD54 YGL163C NPHO23 RTT103 YDR289C NPHO23 SAP30 YMR263W NPHO23 SLK19 YOR195W NPHO23 SMI1 YGR229C NPHO23 VAC14 YLR386W NPHO23 VID22 YLR373C NPHO23 RXT2 RXT2 NPHO23 YDR149C YDR149C NPHO23 YGL211W YGL211W NPHO23 YGL217C YGL217C NPHO23 YML095C-A YML095C-A NPHO23 YNL170W YNL170W NPHO23 YPL017C YPL017C NPHO23 YTA7 YGR270W NPPZ1 AOR1 YBR231C N

Page 147: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

PPZ1 ARP1 YHR129C NPPZ1 ARP6 YLR085C NPPZ1 ASE1 YOR058C NPPZ1 BEM1 YBR200W NPPZ1 BFA1 YJR053W NPPZ1 BIK1 YCL029C NPPZ1 BIM1 YER016W YPPZ1 BUB1 YGR188C NPPZ1 BUB2 YMR055C NPPZ1 BUB3 YOR026W NPPZ1 CHL4 YDR254W NPPZ1 CSM3 YMR048W NPPZ1 CTF19 YPL018W NPPZ1 CTF3 YLR381W NPPZ1 CTF8 YHR191C NPPZ1 DCC1 YCL016C NPPZ1 DYN1 YKR054C NPPZ1 ELP2 YGR200C NPPZ1 FAB1 YFR019W NPPZ1 GIM3 YNL153C NPPZ1 GIM4 YEL003W NPPZ1 GIM5 YML094W NPPZ1 IES2 YNL215W NPPZ1 IML3 YBR107C NPPZ1 INP52 YNL106C NPPZ1 JNM1 YMR294W NPPZ1 KEM1 YGL173C NPPZ1 KIP3 YGL216W NPPZ1 MAD1 YGL086W NPPZ1 MAD2 YJL030W NPPZ1 MAD3 YJL013C NPPZ1 MCK1 YNL307C NPPZ1 MCM21 YDR318W NPPZ1 MCM22 YJR135C NPPZ1 MRC1 YCL060C NPPZ1 NBP2 YDR162C NPPZ1 NUM1 YDR150W NPPZ1 PAC1 YOR269W NPPZ1 PAC11 YDR488C NPPZ1 PHO23 YNL097C NPPZ1 RAD54 YGL163C NPPZ1 RTT103 YDR289C NPPZ1 SAP30 YMR263W NPPZ1 SLK19 YOR195W NPPZ1 SMI1 YGR229C NPPZ1 VAC14 YLR386W NPPZ1 VID22 YLR373C NPPZ1 RXT2 RXT2 NPPZ1 YDR149C YDR149C NPPZ1 YGL211W YGL211W NPPZ1 YGL217C YGL217C NPPZ1 YML095C-A YML095C-A NPPZ1 YNL170W YNL170W NPPZ1 YPL017C YPL017C NPPZ1 YTA7 YGR270W NRAD54 AOR1 YBR231C N/DRAD54 ARP1 YHR129C N/DRAD54 ARP6 YLR085C N/DRAD54 ASE1 YOR058C N/DRAD54 BEM1 YBR200W N/DRAD54 BFA1 YJR053W N/DRAD54 BIK1 YCL029C N/DRAD54 BIM1 YER016W N/DRAD54 BUB1 YGR188C N/DRAD54 BUB2 YMR055C N/DRAD54 BUB3 YOR026W N/D

Page 148: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

RAD54 CHL4 YDR254W N/DRAD54 CSM3 YMR048W N/DRAD54 CTF19 YPL018W N/DRAD54 CTF3 YLR381W N/DRAD54 CTF8 YHR191C N/DRAD54 DCC1 YCL016C N/DRAD54 DYN1 YKR054C N/DRAD54 ELP2 YGR200C N/DRAD54 FAB1 YFR019W N/DRAD54 GIM3 YNL153C N/DRAD54 GIM4 YEL003W N/DRAD54 GIM5 YML094W N/DRAD54 IES2 YNL215W N/DRAD54 IML3 YBR107C N/DRAD54 INP52 YNL106C N/DRAD54 JNM1 YMR294W N/DRAD54 KEM1 YGL173C N/DRAD54 KIP3 YGL216W N/DRAD54 MAD1 YGL086W N/DRAD54 MAD2 YJL030W N/DRAD54 MAD3 YJL013C N/DRAD54 MCK1 YNL307C N/DRAD54 MCM21 YDR318W N/DRAD54 MCM22 YJR135C N/DRAD54 MRC1 YCL060C N/DRAD54 NBP2 YDR162C N/DRAD54 NUM1 YDR150W N/DRAD54 PAC1 YOR269W N/DRAD54 PAC11 YDR488C N/DRAD54 PHO23 YNL097C N/DRAD54 PPZ1 YML016C N/DRAD54 RTT103 YDR289C N/DRAD54 SAP30 YMR263W N/DRAD54 SLK19 YOR195W N/DRAD54 SMI1 YGR229C N/DRAD54 VAC14 YLR386W N/DRAD54 VID22 YLR373C N/DRAD54 RXT2 RXT2 N/DRAD54 YDR149C YDR149C N/DRAD54 YGL211W YGL211W N/DRAD54 YGL217C YGL217C N/DRAD54 YML095C-A YML095C-A N/DRAD54 YNL170W YNL170W N/DRAD54 YPL017C YPL017C N/DRAD54 YTA7 YGR270W N/DRTT103 AOR1 YBR231C NRTT103 ARP1 YHR129C NRTT103 ARP6 YLR085C NRTT103 ASE1 YOR058C NRTT103 BEM1 YBR200W NRTT103 BFA1 YJR053W NRTT103 BIK1 YCL029C YRTT103 BIM1 YER016W YRTT103 BUB1 YGR188C NRTT103 BUB2 YMR055C NRTT103 BUB3 YOR026W NRTT103 CHL4 YDR254W YRTT103 CSM3 YMR048W NRTT103 CTF19 YPL018W NRTT103 CTF3 YLR381W NRTT103 CTF8 YHR191C NRTT103 DCC1 YCL016C NRTT103 DYN1 YKR054C NRTT103 ELP2 YGR200C NRTT103 FAB1 YFR019W NRTT103 GIM3 YNL153C N

Page 149: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

RTT103 GIM4 YEL003W NRTT103 GIM5 YML094W NRTT103 IES2 YNL215W NRTT103 IML3 YBR107C NRTT103 INP52 YNL106C YRTT103 JNM1 YMR294W NRTT103 KEM1 YGL173C NRTT103 KIP3 YGL216W NRTT103 MAD1 YGL086W NRTT103 MAD2 YJL030W NRTT103 MAD3 YJL013C NRTT103 MCK1 YNL307C NRTT103 MCM21 YDR318W NRTT103 MCM22 YJR135C NRTT103 MRC1 YCL060C NRTT103 NBP2 YDR162C NRTT103 NUM1 YDR150W NRTT103 PAC1 YOR269W NRTT103 PAC11 YDR488C NRTT103 PHO23 YNL097C NRTT103 PPZ1 YML016C NRTT103 RAD54 YGL163C NRTT103 SAP30 YMR263W NRTT103 SLK19 YOR195W NRTT103 SMI1 YGR229C NRTT103 VAC14 YLR386W NRTT103 VID22 YLR373C NRTT103 RXT2 RXT2 NRTT103 YDR149C YDR149C NRTT103 YGL211W YGL211W NRTT103 YGL217C YGL217C NRTT103 YML095C-A YML095C-A NRTT103 YNL170W YNL170W NRTT103 YPL017C YPL017C NRTT103 YTA7 YGR270W NSAP30 AOR1 YBR231C NSAP30 ARP1 YHR129C NSAP30 ARP6 YLR085C YSAP30 ASE1 YOR058C NSAP30 BEM1 YBR200W NSAP30 BFA1 YJR053W NSAP30 BIK1 YCL029C NSAP30 BIM1 YER016W YSAP30 BUB1 YGR188C NSAP30 BUB2 YMR055C NSAP30 BUB3 YOR026W NSAP30 CHL4 YDR254W NSAP30 CSM3 YMR048W NSAP30 CTF19 YPL018W NSAP30 CTF3 YLR381W NSAP30 CTF8 YHR191C NSAP30 DCC1 YCL016C NSAP30 DYN1 YKR054C NSAP30 ELP2 YGR200C NSAP30 FAB1 YFR019W NSAP30 GIM3 YNL153C NSAP30 GIM4 YEL003W NSAP30 GIM5 YML094W NSAP30 IES2 YNL215W YSAP30 IML3 YBR107C NSAP30 INP52 YNL106C NSAP30 JNM1 YMR294W NSAP30 KEM1 YGL173C YSAP30 KIP3 YGL216W NSAP30 MAD1 YGL086W NSAP30 MAD2 YJL030W N

Page 150: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

SAP30 MAD3 YJL013C NSAP30 MCK1 YNL307C NSAP30 MCM21 YDR318W NSAP30 MCM22 YJR135C NSAP30 MRC1 YCL060C NSAP30 NBP2 YDR162C NSAP30 NUM1 YDR150W NSAP30 PAC1 YOR269W NSAP30 PAC11 YDR488C NSAP30 PHO23 YNL097C NSAP30 PPZ1 YML016C NSAP30 RAD54 YGL163C NSAP30 RTT103 YDR289C NSAP30 SLK19 YOR195W NSAP30 SMI1 YGR229C NSAP30 VAC14 YLR386W NSAP30 VID22 YLR373C NSAP30 RXT2 RXT2 NSAP30 YDR149C YDR149C NSAP30 YGL211W YGL211W NSAP30 YGL217C YGL217C NSAP30 YML095C-A YML095C-A NSAP30 YNL170W YNL170W NSAP30 YPL017C YPL017C NSAP30 YTA7 YGR270W NSLK19 AOR1 YBR231C NSLK19 ARP1 YHR129C NSLK19 ARP6 YLR085C NSLK19 ASE1 YOR058C NSLK19 BEM1 YBR200W NSLK19 BFA1 YJR053W NSLK19 BIK1 YCL029C NSLK19 BIM1 YER016W YSLK19 BUB1 YGR188C YSLK19 BUB2 YMR055C NSLK19 BUB3 YOR026W YSLK19 CHL4 YDR254W NSLK19 CSM3 YMR048W NSLK19 CTF19 YPL018W NSLK19 CTF3 YLR381W NSLK19 CTF8 YHR191C YSLK19 DCC1 YCL016C NSLK19 DYN1 YKR054C NSLK19 ELP2 YGR200C NSLK19 FAB1 YFR019W NSLK19 GIM3 YNL153C NSLK19 GIM4 YEL003W NSLK19 GIM5 YML094W NSLK19 IES2 YNL215W NSLK19 IML3 YBR107C NSLK19 INP52 YNL106C NSLK19 JNM1 YMR294W NSLK19 KEM1 YGL173C NSLK19 KIP3 YGL216W NSLK19 MAD1 YGL086W YSLK19 MAD2 YJL030W NSLK19 MAD3 YJL013C NSLK19 MCK1 YNL307C NSLK19 MCM21 YDR318W NSLK19 MCM22 YJR135C NSLK19 MRC1 YCL060C NSLK19 NBP2 YDR162C NSLK19 NUM1 YDR150W NSLK19 PAC1 YOR269W NSLK19 PAC11 YDR488C NSLK19 PHO23 YNL097C N

Page 151: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

SLK19 PPZ1 YML016C NSLK19 RAD54 YGL163C NSLK19 RTT103 YDR289C NSLK19 SAP30 YMR263W NSLK19 SMI1 YGR229C NSLK19 VAC14 YLR386W NSLK19 VID22 YLR373C NSLK19 RXT2 RXT2 NSLK19 YDR149C YDR149C NSLK19 YGL211W YGL211W NSLK19 YGL217C YGL217C NSLK19 YML095C-A YML095C-A NSLK19 YNL170W YNL170W NSLK19 YPL017C YPL017C NSLK19 YTA7 YGR270W NSMI1 AOR1 YBR231C NSMI1 ARP1 YHR129C NSMI1 ARP6 YLR085C NSMI1 ASE1 YOR058C NSMI1 BEM1 YBR200W YSMI1 BFA1 YJR053W NSMI1 BIK1 YCL029C NSMI1 BIM1 YER016W YSMI1 BUB1 YGR188C NSMI1 BUB2 YMR055C NSMI1 BUB3 YOR026W NSMI1 CHL4 YDR254W NSMI1 CSM3 YMR048W NSMI1 CTF19 YPL018W NSMI1 CTF3 YLR381W NSMI1 CTF8 YHR191C NSMI1 DCC1 YCL016C NSMI1 DYN1 YKR054C NSMI1 ELP2 YGR200C NSMI1 FAB1 YFR019W NSMI1 GIM3 YNL153C NSMI1 GIM4 YEL003W NSMI1 GIM5 YML094W NSMI1 IES2 YNL215W NSMI1 IML3 YBR107C NSMI1 INP52 YNL106C NSMI1 JNM1 YMR294W NSMI1 KEM1 YGL173C NSMI1 KIP3 YGL216W NSMI1 MAD1 YGL086W NSMI1 MAD2 YJL030W NSMI1 MAD3 YJL013C NSMI1 MCK1 YNL307C NSMI1 MCM21 YDR318W NSMI1 MCM22 YJR135C NSMI1 MRC1 YCL060C NSMI1 NBP2 YDR162C NSMI1 NUM1 YDR150W NSMI1 PAC1 YOR269W NSMI1 PAC11 YDR488C NSMI1 PHO23 YNL097C NSMI1 PPZ1 YML016C NSMI1 RAD54 YGL163C NSMI1 RTT103 YDR289C NSMI1 SAP30 YMR263W NSMI1 SLK19 YOR195W NSMI1 VAC14 YLR386W NSMI1 VID22 YLR373C NSMI1 RXT2 RXT2 NSMI1 YDR149C YDR149C NSMI1 YGL211W YGL211W N

Page 152: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

SMI1 YGL217C YGL217C NSMI1 YML095C-A YML095C-A NSMI1 YNL170W YNL170W NSMI1 YPL017C YPL017C NSMI1 YTA7 YGR270W NVAC14 AOR1 YBR231C NVAC14 ARP1 YHR129C NVAC14 ARP6 YLR085C NVAC14 ASE1 YOR058C NVAC14 BEM1 YBR200W NVAC14 BFA1 YJR053W NVAC14 BIK1 YCL029C NVAC14 BIM1 YER016W YVAC14 BUB1 YGR188C NVAC14 BUB2 YMR055C NVAC14 BUB3 YOR026W NVAC14 CHL4 YDR254W NVAC14 CSM3 YMR048W NVAC14 CTF19 YPL018W NVAC14 CTF3 YLR381W YVAC14 CTF8 YHR191C NVAC14 DCC1 YCL016C NVAC14 DYN1 YKR054C NVAC14 ELP2 YGR200C NVAC14 FAB1 YFR019W NVAC14 GIM3 YNL153C YVAC14 GIM4 YEL003W NVAC14 GIM5 YML094W NVAC14 IES2 YNL215W NVAC14 IML3 YBR107C NVAC14 INP52 YNL106C NVAC14 JNM1 YMR294W NVAC14 KEM1 YGL173C NVAC14 KIP3 YGL216W NVAC14 MAD1 YGL086W NVAC14 MAD2 YJL030W NVAC14 MAD3 YJL013C NVAC14 MCK1 YNL307C NVAC14 MCM21 YDR318W NVAC14 MCM22 YJR135C NVAC14 MRC1 YCL060C NVAC14 NBP2 YDR162C NVAC14 NUM1 YDR150W NVAC14 PAC1 YOR269W NVAC14 PAC11 YDR488C NVAC14 PHO23 YNL097C NVAC14 PPZ1 YML016C NVAC14 RAD54 YGL163C NVAC14 RTT103 YDR289C NVAC14 SAP30 YMR263W NVAC14 SLK19 YOR195W NVAC14 SMI1 YGR229C NVAC14 VID22 YLR373C NVAC14 RXT2 RXT2 NVAC14 YDR149C YDR149C NVAC14 YGL211W YGL211W NVAC14 YGL217C YGL217C NVAC14 YML095C-A YML095C-A NVAC14 YNL170W YNL170W NVAC14 YPL017C YPL017C NVAC14 YTA7 YGR270W NVID22 AOR1 YBR231C NVID22 ARP1 YHR129C NVID22 ARP6 YLR085C NVID22 ASE1 YOR058C NVID22 BEM1 YBR200W Y

Page 153: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

VID22 BFA1 YJR053W NVID22 BIK1 YCL029C NVID22 BIM1 YER016W YVID22 BUB1 YGR188C YVID22 BUB2 YMR055C NVID22 BUB3 YOR026W YVID22 CHL4 YDR254W NVID22 CSM3 YMR048W NVID22 CTF19 YPL018W NVID22 CTF3 YLR381W YVID22 CTF8 YHR191C YVID22 DCC1 YCL016C NVID22 DYN1 YKR054C NVID22 ELP2 YGR200C NVID22 FAB1 YFR019W NVID22 GIM3 YNL153C NVID22 GIM4 YEL003W NVID22 GIM5 YML094W NVID22 IES2 YNL215W NVID22 IML3 YBR107C NVID22 INP52 YNL106C NVID22 JNM1 YMR294W NVID22 KEM1 YGL173C YVID22 KIP3 YGL216W NVID22 MAD1 YGL086W NVID22 MAD2 YJL030W NVID22 MAD3 YJL013C NVID22 MCK1 YNL307C NVID22 MCM21 YDR318W NVID22 MCM22 YJR135C NVID22 MRC1 YCL060C NVID22 NBP2 YDR162C NVID22 NUM1 YDR150W NVID22 PAC1 YOR269W NVID22 PAC11 YDR488C NVID22 PHO23 YNL097C NVID22 PPZ1 YML016C NVID22 RAD54 YGL163C NVID22 RTT103 YDR289C NVID22 SAP30 YMR263W NVID22 SLK19 YOR195W NVID22 SMI1 YGR229C NVID22 VAC14 YLR386W YVID22 RXT2 RXT2 NVID22 YDR149C YDR149C NVID22 YGL211W YGL211W NVID22 YGL217C YGL217C NVID22 YML095C-A YML095C-A NVID22 YNL170W YNL170W YVID22 YPL017C YPL017C NVID22 YTA7 YGR270W NRXT2 AOR1 YBR231C NRXT2 ARP1 YHR129C NRXT2 ARP6 YLR085C YRXT2 ASE1 YOR058C NRXT2 BEM1 YBR200W NRXT2 BFA1 YJR053W NRXT2 BIK1 YCL029C NRXT2 BIM1 YER016W YRXT2 BUB1 YGR188C NRXT2 BUB2 YMR055C NRXT2 BUB3 YOR026W NRXT2 CHL4 YDR254W NRXT2 CSM3 YMR048W NRXT2 CTF19 YPL018W NRXT2 CTF3 YLR381W N

Page 154: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

RXT2 CTF8 YHR191C NRXT2 DCC1 YCL016C NRXT2 DYN1 YKR054C NRXT2 ELP2 YGR200C NRXT2 FAB1 YFR019W NRXT2 GIM3 YNL153C YRXT2 GIM4 YEL003W NRXT2 GIM5 YML094W NRXT2 IES2 YNL215W YRXT2 IML3 YBR107C YRXT2 INP52 YNL106C NRXT2 JNM1 YMR294W NRXT2 KEM1 YGL173C NRXT2 KIP3 YGL216W NRXT2 MAD1 YGL086W NRXT2 MAD2 YJL030W NRXT2 MAD3 YJL013C NRXT2 MCK1 YNL307C NRXT2 MCM21 YDR318W NRXT2 MCM22 YJR135C NRXT2 MRC1 YCL060C NRXT2 NBP2 YDR162C NRXT2 NUM1 YDR150W NRXT2 PAC1 YOR269W NRXT2 PAC11 YDR488C NRXT2 PHO23 YNL097C NRXT2 PPZ1 YML016C NRXT2 RAD54 YGL163C NRXT2 RTT103 YDR289C NRXT2 SAP30 YMR263W NRXT2 SLK19 YOR195W NRXT2 SMI1 YGR229C NRXT2 VAC14 YLR386W NRXT2 VID22 YLR373C NRXT2 YDR149C YDR149C NRXT2 YGL211W YGL211W NRXT2 YGL217C YGL217C NRXT2 YML095C-A YML095C-A NRXT2 YNL170W YNL170W NRXT2 YPL017C YPL017C NRXT2 YTA7 YGR270W NYDR149C AOR1 YBR231C NYDR149C ARP1 YHR129C NYDR149C ARP6 YLR085C NYDR149C ASE1 YOR058C NYDR149C BEM1 YBR200W NYDR149C BFA1 YJR053W NYDR149C BIK1 YCL029C NYDR149C BIM1 YER016W YYDR149C BUB1 YGR188C NYDR149C BUB2 YMR055C NYDR149C BUB3 YOR026W NYDR149C CHL4 YDR254W NYDR149C CSM3 YMR048W NYDR149C CTF19 YPL018W NYDR149C CTF3 YLR381W NYDR149C CTF8 YHR191C NYDR149C DCC1 YCL016C NYDR149C DYN1 YKR054C NYDR149C ELP2 YGR200C NYDR149C FAB1 YFR019W YYDR149C GIM3 YNL153C NYDR149C GIM4 YEL003W NYDR149C GIM5 YML094W YYDR149C IES2 YNL215W NYDR149C IML3 YBR107C N

Page 155: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

YDR149C INP52 YNL106C NYDR149C JNM1 YMR294W NYDR149C KEM1 YGL173C NYDR149C KIP3 YGL216W YYDR149C MAD1 YGL086W NYDR149C MAD2 YJL030W NYDR149C MAD3 YJL013C NYDR149C MCK1 YNL307C NYDR149C MCM21 YDR318W NYDR149C MCM22 YJR135C NYDR149C MRC1 YCL060C NYDR149C NBP2 YDR162C YYDR149C NUM1 YDR150W YYDR149C PAC1 YOR269W NYDR149C PAC11 YDR488C NYDR149C PHO23 YNL097C NYDR149C PPZ1 YML016C NYDR149C RAD54 YGL163C NYDR149C RTT103 YDR289C NYDR149C SAP30 YMR263W NYDR149C SLK19 YOR195W NYDR149C SMI1 YGR229C NYDR149C VAC14 YLR386W NYDR149C VID22 YLR373C NYDR149C RXT2 RXT2 NYDR149C YGL211W YGL211W NYDR149C YGL217C YGL217C YYDR149C YML095C-A YML095C-A NYDR149C YNL170W YNL170W NYDR149C YPL017C YPL017C NYDR149C YTA7 YGR270W NYGL211w AOR1 YBR231C NYGL211w ARP1 YHR129C NYGL211w ARP6 YLR085C NYGL211w ASE1 YOR058C NYGL211w BEM1 YBR200W YYGL211w BFA1 YJR053W NYGL211w BIK1 YCL029C NYGL211w BIM1 YER016W YYGL211w BUB1 YGR188C NYGL211w BUB2 YMR055C NYGL211w BUB3 YOR026W NYGL211w CHL4 YDR254W NYGL211w CSM3 YMR048W NYGL211w CTF19 YPL018W NYGL211w CTF3 YLR381W NYGL211w CTF8 YHR191C NYGL211w DCC1 YCL016C NYGL211w DYN1 YKR054C NYGL211w ELP2 YGR200C NYGL211w FAB1 YFR019W NYGL211w GIM3 YNL153C NYGL211w GIM4 YEL003W NYGL211w GIM5 YML094W NYGL211w IES2 YNL215W NYGL211w IML3 YBR107C NYGL211w INP52 YNL106C NYGL211w JNM1 YMR294W NYGL211w KEM1 YGL173C YYGL211w KIP3 YGL216W YYGL211w MAD1 YGL086W NYGL211w MAD2 YJL030W NYGL211w MAD3 YJL013C NYGL211w MCK1 YNL307C NYGL211w MCM21 YDR318W NYGL211w MCM22 YJR135C N

Page 156: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

YGL211w MRC1 YCL060C NYGL211w NBP2 YDR162C YYGL211w NUM1 YDR150W NYGL211w PAC1 YOR269W NYGL211w PAC11 YDR488C NYGL211w PHO23 YNL097C NYGL211w PPZ1 YML016C NYGL211w RAD54 YGL163C NYGL211w RTT103 YDR289C NYGL211w SAP30 YMR263W NYGL211w SLK19 YOR195W NYGL211w SMI1 YGR229C NYGL211w VAC14 YLR386W NYGL211w VID22 YLR373C NYGL211w RXT2 RXT2 NYGL211w YDR149C YDR149C NYGL211w YGL217C YGL217C YYGL211w YML095C-A YML095C-A NYGL211w YNL170W YNL170W NYGL211w YPL017C YPL017C NYGL211w YTA7 YGR270W NYGL217C AOR1 YBR231C NYGL217C ARP1 YHR129C YYGL217C ARP6 YLR085C NYGL217C ASE1 YOR058C NYGL217C BEM1 YBR200W NYGL217C BFA1 YJR053W NYGL217C BIK1 YCL029C NYGL217C BIM1 YER016W YYGL217C BUB1 YGR188C YYGL217C BUB2 YMR055C NYGL217C BUB3 YOR026W YYGL217C CHL4 YDR254W NYGL217C CSM3 YMR048W NYGL217C CTF19 YPL018W NYGL217C CTF3 YLR381W NYGL217C CTF8 YHR191C NYGL217C DCC1 YCL016C NYGL217C DYN1 YKR054C NYGL217C ELP2 YGR200C NYGL217C FAB1 YFR019W NYGL217C GIM3 YNL153C NYGL217C GIM4 YEL003W NYGL217C GIM5 YML094W NYGL217C IES2 YNL215W NYGL217C IML3 YBR107C NYGL217C INP52 YNL106C NYGL217C JNM1 YMR294W YYGL217C KEM1 YGL173C YYGL217C KIP3 YGL216W YYGL217C MAD1 YGL086W NYGL217C MAD2 YJL030W NYGL217C MAD3 YJL013C NYGL217C MCK1 YNL307C NYGL217C MCM21 YDR318W NYGL217C MCM22 YJR135C NYGL217C MRC1 YCL060C NYGL217C NBP2 YDR162C YYGL217C NUM1 YDR150W YYGL217C PAC1 YOR269W YYGL217C PAC11 YDR488C NYGL217C PHO23 YNL097C NYGL217C PPZ1 YML016C NYGL217C RAD54 YGL163C NYGL217C RTT103 YDR289C NYGL217C SAP30 YMR263W N

Page 157: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

YGL217C SLK19 YOR195W NYGL217C SMI1 YGR229C NYGL217C VAC14 YLR386W NYGL217C VID22 YLR373C NYGL217C RXT2 RXT2 NYGL217C YDR149C YDR149C YYGL217C YGL211W YGL211W YYGL217C YML095C-A YML095C-A NYGL217C YNL170W YNL170W NYGL217C YPL017C YPL017C NYGL217C YTA7 YGR270W NYML095C-A AOR1 YBR231C YYML095C-A ARP1 YHR129C YYML095C-A ARP6 YLR085C YYML095C-A ASE1 YOR058C YYML095C-A BEM1 YBR200W YYML095C-A BFA1 YJR053W YYML095C-A BIK1 YCL029C YYML095C-A BIM1 YER016W YYML095C-A BUB1 YGR188C YYML095C-A BUB2 YMR055C YYML095C-A BUB3 YOR026W YYML095C-A CHL4 YDR254W NYML095C-A CSM3 YMR048W NYML095C-A CTF19 YPL018W YYML095C-A CTF3 YLR381W NYML095C-A CTF8 YHR191C YYML095C-A DCC1 YCL016C YYML095C-A DYN1 YKR054C YYML095C-A ELP2 YGR200C NYML095C-A FAB1 YFR019W YYML095C-A GIM3 YNL153C NYML095C-A GIM4 YEL003W NYML095C-A GIM5 YML094W YYML095C-A IES2 YNL215W NYML095C-A IML3 YBR107C NYML095C-A INP52 YNL106C YYML095C-A JNM1 YMR294W YYML095C-A KEM1 YGL173C YYML095C-A KIP3 YGL216W NYML095C-A MAD1 YGL086W YYML095C-A MAD2 YJL030W YYML095C-A MAD3 YJL013C NYML095C-A MCK1 YNL307C NYML095C-A MCM21 YDR318W YYML095C-A MCM22 YJR135C NYML095C-A MRC1 YCL060C NYML095C-A NBP2 YDR162C NYML095C-A NUM1 YDR150W YYML095C-A PAC1 YOR269W NYML095C-A PAC11 YDR488C YYML095C-A PHO23 YNL097C NYML095C-A PPZ1 YML016C NYML095C-A RAD54 YGL163C NYML095C-A RTT103 YDR289C NYML095C-A SAP30 YMR263W NYML095C-A SLK19 YOR195W NYML095C-A SMI1 YGR229C YYML095C-A VAC14 YLR386W YYML095C-A VID22 YLR373C NYML095C-A RXT2 RXT2 NYML095C-A YDR149C YDR149C YYML095C-A YGL211W YGL211W NYML095C-A YGL217C YGL217C NYML095C-A YNL170W YNL170W NYML095C-A YPL017C YPL017C N

Page 158: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

YML095C-A YTA7 YGR270W NYNL170W AOR1 YBR231C NYNL170W ARP1 YHR129C NYNL170W ARP6 YLR085C NYNL170W ASE1 YOR058C NYNL170W BEM1 YBR200W NYNL170W BFA1 YJR053W NYNL170W BIK1 YCL029C NYNL170W BIM1 YER016W YYNL170W BUB1 YGR188C NYNL170W BUB2 YMR055C NYNL170W BUB3 YOR026W NYNL170W CHL4 YDR254W NYNL170W CSM3 YMR048W NYNL170W CTF19 YPL018W NYNL170W CTF3 YLR381W NYNL170W CTF8 YHR191C NYNL170W DCC1 YCL016C NYNL170W DYN1 YKR054C NYNL170W ELP2 YGR200C NYNL170W FAB1 YFR019W NYNL170W GIM3 YNL153C YYNL170W GIM4 YEL003W NYNL170W GIM5 YML094W NYNL170W IES2 YNL215W YYNL170W IML3 YBR107C NYNL170W INP52 YNL106C YYNL170W JNM1 YMR294W NYNL170W KEM1 YGL173C NYNL170W KIP3 YGL216W NYNL170W MAD1 YGL086W NYNL170W MAD2 YJL030W NYNL170W MAD3 YJL013C NYNL170W MCK1 YNL307C NYNL170W MCM21 YDR318W NYNL170W MCM22 YJR135C NYNL170W MRC1 YCL060C NYNL170W NBP2 YDR162C YYNL170W NUM1 YDR150W NYNL170W PAC1 YOR269W NYNL170W PAC11 YDR488C NYNL170W PHO23 YNL097C NYNL170W PPZ1 YML016C NYNL170W RAD54 YGL163C NYNL170W RTT103 YDR289C NYNL170W SAP30 YMR263W NYNL170W SLK19 YOR195W NYNL170W SMI1 YGR229C NYNL170W VAC14 YLR386W NYNL170W VID22 YLR373C YYNL170W RXT2 RXT2 NYNL170W YDR149C YDR149C NYNL170W YGL211W YGL211W NYNL170W YGL217C YGL217C NYNL170W YML095C-A YML095C-A NYNL170W YPL017C YPL017C NYNL170W YTA7 YGR270W NYPL017C AOR1 YBR231C NYPL017C ARP1 YHR129C NYPL017C ARP6 YLR085C NYPL017C ASE1 YOR058C NYPL017C BEM1 YBR200W NYPL017C BFA1 YJR053W NYPL017C BIK1 YCL029C NYPL017C BIM1 YER016W YYPL017C BUB1 YGR188C N

Page 159: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

YPL017C BUB2 YMR055C NYPL017C BUB3 YOR026W NYPL017C CHL4 YDR254W NYPL017C CSM3 YMR048W NYPL017C CTF19 YPL018W YYPL017C CTF3 YLR381W NYPL017C CTF8 YHR191C NYPL017C DCC1 YCL016C NYPL017C DYN1 YKR054C NYPL017C ELP2 YGR200C NYPL017C FAB1 YFR019W NYPL017C GIM3 YNL153C NYPL017C GIM4 YEL003W NYPL017C GIM5 YML094W NYPL017C IES2 YNL215W NYPL017C IML3 YBR107C NYPL017C INP52 YNL106C NYPL017C JNM1 YMR294W NYPL017C KEM1 YGL173C NYPL017C KIP3 YGL216W NYPL017C MAD1 YGL086W NYPL017C MAD2 YJL030W NYPL017C MAD3 YJL013C NYPL017C MCK1 YNL307C NYPL017C MCM21 YDR318W NYPL017C MCM22 YJR135C NYPL017C MRC1 YCL060C NYPL017C NBP2 YDR162C NYPL017C NUM1 YDR150W NYPL017C PAC1 YOR269W NYPL017C PAC11 YDR488C NYPL017C PHO23 YNL097C NYPL017C PPZ1 YML016C NYPL017C RAD54 YGL163C NYPL017C RTT103 YDR289C NYPL017C SAP30 YMR263W NYPL017C SLK19 YOR195W NYPL017C SMI1 YGR229C NYPL017C VAC14 YLR386W NYPL017C VID22 YLR373C NYPL017C RXT2 RXT2 NYPL017C YDR149C YDR149C NYPL017C YGL211W YGL211W NYPL017C YGL217C YGL217C NYPL017C YML095C-A YML095C-A NYPL017C YNL170W YNL170W NYPL017C YTA7 YGR270W NYTA7 AOR1 YBR231C YYTA7 ARP1 YHR129C NYTA7 ARP6 YLR085C YYTA7 ASE1 YOR058C NYTA7 BEM1 YBR200W NYTA7 BFA1 YJR053W NYTA7 BIK1 YCL029C NYTA7 BIM1 YER016W YYTA7 BUB1 YGR188C YYTA7 BUB2 YMR055C NYTA7 BUB3 YOR026W YYTA7 CHL4 YDR254W NYTA7 CSM3 YMR048W NYTA7 CTF19 YPL018W NYTA7 CTF3 YLR381W NYTA7 CTF8 YHR191C NYTA7 DCC1 YCL016C NYTA7 DYN1 YKR054C NYTA7 ELP2 YGR200C N

Page 160: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

YTA7 FAB1 YFR019W NYTA7 GIM3 YNL153C NYTA7 GIM4 YEL003W NYTA7 GIM5 YML094W YYTA7 IES2 YNL215W NYTA7 IML3 YBR107C NYTA7 INP52 YNL106C NYTA7 JNM1 YMR294W NYTA7 KEM1 YGL173C NYTA7 KIP3 YGL216W NYTA7 MAD1 YGL086W NYTA7 MAD2 YJL030W NYTA7 MAD3 YJL013C NYTA7 MCK1 YNL307C NYTA7 MCM21 YDR318W NYTA7 MCM22 YJR135C NYTA7 MRC1 YCL060C NYTA7 NBP2 YDR162C NYTA7 NUM1 YDR150W NYTA7 PAC1 YOR269W NYTA7 PAC11 YDR488C NYTA7 PHO23 YNL097C NYTA7 PPZ1 YML016C NYTA7 RAD54 YGL163C NYTA7 RTT103 YDR289C NYTA7 SAP30 YMR263W NYTA7 SLK19 YOR195W NYTA7 SMI1 YGR229C NYTA7 VAC14 YLR386W NYTA7 VID22 YLR373C NYTA7 RXT2 RXT2 NYTA7 YDR149C YDR149C NYTA7 YGL211W YGL211W NYTA7 YGL217C YGL217C NYTA7 YML095C-A YML095C-A NYTA7 YNL170W YNL170W NYTA7 YPL017C YPL017C NBUD27 CAC2 YML102W NBUD27 CSM3 YMR048W NBUD27 CTF4 YPR135W NBUD27 DDC1 YPL194W NBUD27 DOC1 YGL240W NBUD27 ESC2 YDR363W NBUD27 EXO1 YOR033C NBUD27 HPC2 YBR215W NBUD27 HPR5 YJL092W NBUD27 HST1 YOL068C NBUD27 HST3 YOR025W NBUD27 LYS7 YMR038C NBUD27 MMS4 YBR098W NBUD27 MRE11 YMR224C NBUD27 MUS81 YDR386W NBUD27 RAD17 YOR368W NBUD27 RAD24 YER173W NBUD27 RAD27 YKL113C YBUD27 RAD50 YNL250W NBUD27 RAD51 YER095W NBUD27 RAD52 YML032C NBUD27 RAD54 YGL163C NBUD27 RAD55 YDR076W NBUD27 RAD57 YDR004W NBUD27 RAD9 YDR217C NBUD27 RPL27A YHR010W NBUD27 RPS30B YOR182C NBUD27 SAE2 YGL175C NBUD27 SGS1 YMR190C N

Page 161: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

BUD27 SIS2 YKR072C NBUD27 SOD1 YJR104C YBUD27 XRS2 YDR369C NBUD27 YDJ1 YNL064C YBUD27 YLR352W YLR352W NBUD27 YNL171C YNL171C NBUD27 YPR116W YPR116W N/DCAC2 BUD27 YFL023W NCAC2 CSM3 YMR048W NCAC2 CTF4 YPR135W NCAC2 DDC1 YPL194W NCAC2 DOC1 YGL240W NCAC2 ESC2 YDR363W NCAC2 EXO1 YOR033C NCAC2 HPC2 YBR215W NCAC2 HPR5 YJL092W NCAC2 HST1 YOL068C NCAC2 HST3 YOR025W NCAC2 LYS7 YMR038C NCAC2 MMS4 YBR098W NCAC2 MRE11 YMR224C YCAC2 MUS81 YDR386W NCAC2 RAD17 YOR368W NCAC2 RAD24 YER173W NCAC2 RAD27 YKL113C YCAC2 RAD50 YNL250W NCAC2 RAD51 YER095W NCAC2 RAD52 YML032C NCAC2 RAD54 YGL163C NCAC2 RAD55 YDR076W NCAC2 RAD57 YDR004W NCAC2 RAD9 YDR217C NCAC2 RPL27A YHR010W NCAC2 RPS30B YOR182C NCAC2 SAE2 YGL175C NCAC2 SGS1 YMR190C NCAC2 SIS2 YKR072C NCAC2 SOD1 YJR104C NCAC2 XRS2 YDR369C YCAC2 YDJ1 YNL064C NCAC2 YLR352W YLR352W NCAC2 YNL171C YNL171C YCAC2 YPR116W YPR116W N/DCSM3 BUD27 YFL023W NCSM3 CAC2 YML102W NCSM3 CTF4 YPR135W YCSM3 DDC1 YPL194W NCSM3 DOC1 YGL240W NCSM3 ESC2 YDR363W NCSM3 EXO1 YOR033C NCSM3 HPC2 YBR215W NCSM3 HPR5 YJL092W YCSM3 HST1 YOL068C NCSM3 HST3 YOR025W NCSM3 LYS7 YMR038C YCSM3 MMS4 YBR098W NCSM3 MRE11 YMR224C NCSM3 MUS81 YDR386W NCSM3 RAD17 YOR368W NCSM3 RAD24 YER173W NCSM3 RAD27 YKL113C YCSM3 RAD50 YNL250W NCSM3 RAD51 YER095W NCSM3 RAD52 YML032C NCSM3 RAD54 YGL163C NCSM3 RAD55 YDR076W N

Page 162: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

CSM3 RAD57 YDR004W NCSM3 RAD9 YDR217C NCSM3 RPL27A YHR010W NCSM3 RPS30B YOR182C NCSM3 SAE2 YGL175C NCSM3 SGS1 YMR190C YCSM3 SIS2 YKR072C NCSM3 SOD1 YJR104C NCSM3 XRS2 YDR369C NCSM3 YDJ1 YNL064C NCSM3 YLR352W YLR352W NCSM3 YNL171C YNL171C YCSM3 YPR116W YPR116W N/DCTF4 BUD27 YFL023W NCTF4 CAC2 YML102W YCTF4 CSM3 YMR048W YCTF4 DDC1 YPL194W NCTF4 DOC1 YGL240W NCTF4 ESC2 YDR363W NCTF4 EXO1 YOR033C NCTF4 HPC2 YBR215W NCTF4 HPR5 YJL092W YCTF4 HST1 YOL068C NCTF4 HST3 YOR025W NCTF4 LYS7 YMR038C NCTF4 MMS4 YBR098W NCTF4 MRE11 YMR224C YCTF4 MUS81 YDR386W NCTF4 RAD17 YOR368W NCTF4 RAD24 YER173W NCTF4 RAD27 YKL113C YCTF4 RAD50 YNL250W YCTF4 RAD51 YER095W NCTF4 RAD52 YML032C NCTF4 RAD54 YGL163C NCTF4 RAD55 YDR076W NCTF4 RAD57 YDR004W NCTF4 RAD9 YDR217C NCTF4 RPL27A YHR010W YCTF4 RPS30B YOR182C NCTF4 SAE2 YGL175C NCTF4 SGS1 YMR190C NCTF4 SIS2 YKR072C NCTF4 SOD1 YJR104C YCTF4 XRS2 YDR369C YCTF4 YDJ1 YNL064C NCTF4 YLR352W YLR352W NCTF4 YNL171C YNL171C YCTF4 YPR116W YPR116W N/DDDC1 BUD27 YFL023W NDDC1 CAC2 YML102W NDDC1 CSM3 YMR048W NDDC1 CTF4 YPR135W NDDC1 DOC1 YGL240W NDDC1 ESC2 YDR363W NDDC1 EXO1 YOR033C NDDC1 HPC2 YBR215W NDDC1 HPR5 YJL092W NDDC1 HST1 YOL068C NDDC1 HST3 YOR025W NDDC1 LYS7 YMR038C NDDC1 MMS4 YBR098W NDDC1 MRE11 YMR224C NDDC1 MUS81 YDR386W NDDC1 RAD17 YOR368W NDDC1 RAD24 YER173W N

Page 163: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

DDC1 RAD27 YKL113C YDDC1 RAD50 YNL250W NDDC1 RAD51 YER095W NDDC1 RAD52 YML032C NDDC1 RAD54 YGL163C NDDC1 RAD55 YDR076W NDDC1 RAD57 YDR004W NDDC1 RAD9 YDR217C NDDC1 RPL27A YHR010W NDDC1 RPS30B YOR182C NDDC1 SAE2 YGL175C NDDC1 SGS1 YMR190C NDDC1 SIS2 YKR072C NDDC1 SOD1 YJR104C YDDC1 XRS2 YDR369C NDDC1 YDJ1 YNL064C NDDC1 YLR352W YLR352W NDDC1 YNL171C YNL171C NDDC1 YPR116W YPR116W N/DDOC1 BUD27 YFL023W NDOC1 CAC2 YML102W NDOC1 CSM3 YMR048W NDOC1 CTF4 YPR135W YDOC1 DDC1 YPL194W NDOC1 ESC2 YDR363W NDOC1 EXO1 YOR033C NDOC1 HPC2 YBR215W NDOC1 HPR5 YJL092W YDOC1 HST1 YOL068C NDOC1 HST3 YOR025W NDOC1 LYS7 YMR038C NDOC1 MMS4 YBR098W NDOC1 MRE11 YMR224C YDOC1 MUS81 YDR386W NDOC1 RAD17 YOR368W NDOC1 RAD24 YER173W NDOC1 RAD27 YKL113C YDOC1 RAD50 YNL250W NDOC1 RAD51 YER095W NDOC1 RAD52 YML032C YDOC1 RAD54 YGL163C NDOC1 RAD55 YDR076W NDOC1 RAD57 YDR004W NDOC1 RAD9 YDR217C NDOC1 RPL27A YHR010W YDOC1 RPS30B YOR182C NDOC1 SAE2 YGL175C NDOC1 SGS1 YMR190C NDOC1 SIS2 YKR072C NDOC1 SOD1 YJR104C NDOC1 XRS2 YDR369C NDOC1 YDJ1 YNL064C NDOC1 YLR352W YLR352W NDOC1 YNL171C YNL171C YDOC1 YPR116W YPR116W N/DESC2 BUD27 YFL023W NESC2 CAC2 YML102W NESC2 CSM3 YMR048W NESC2 CTF4 YPR135W NESC2 DDC1 YPL194W NESC2 DOC1 YGL240W NESC2 EXO1 YOR033C NESC2 HPC2 YBR215W YESC2 HPR5 YJL092W YESC2 HST1 YOL068C NESC2 HST3 YOR025W N

Page 164: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

ESC2 LYS7 YMR038C YESC2 MMS4 YBR098W YESC2 MRE11 YMR224C NESC2 MUS81 YDR386W YESC2 RAD17 YOR368W NESC2 RAD24 YER173W NESC2 RAD27 YKL113C YESC2 RAD50 YNL250W NESC2 RAD51 YER095W NESC2 RAD52 YML032C NESC2 RAD54 YGL163C NESC2 RAD55 YDR076W NESC2 RAD57 YDR004W NESC2 RAD9 YDR217C NESC2 RPL27A YHR010W NESC2 RPS30B YOR182C NESC2 SAE2 YGL175C NESC2 SGS1 YMR190C YESC2 SIS2 YKR072C NESC2 SOD1 YJR104C NESC2 XRS2 YDR369C YESC2 YDJ1 YNL064C NESC2 YLR352W YLR352W NESC2 YNL171C YNL171C NESC2 YPR116W YPR116W N/DEXO1 BUD27 YFL023W NEXO1 CAC2 YML102W NEXO1 CSM3 YMR048W NEXO1 CTF4 YPR135W NEXO1 DDC1 YPL194W NEXO1 DOC1 YGL240W NEXO1 ESC2 YDR363W NEXO1 HPC2 YBR215W NEXO1 HPR5 YJL092W NEXO1 HST1 YOL068C NEXO1 HST3 YOR025W YEXO1 LYS7 YMR038C NEXO1 MMS4 YBR098W NEXO1 MRE11 YMR224C NEXO1 MUS81 YDR386W NEXO1 RAD17 YOR368W NEXO1 RAD24 YER173W NEXO1 RAD27 YKL113C YEXO1 RAD50 YNL250W NEXO1 RAD51 YER095W NEXO1 RAD52 YML032C NEXO1 RAD54 YGL163C NEXO1 RAD55 YDR076W NEXO1 RAD57 YDR004W NEXO1 RAD9 YDR217C NEXO1 RPL27A YHR010W NEXO1 RPS30B YOR182C NEXO1 SAE2 YGL175C NEXO1 SGS1 YMR190C NEXO1 SIS2 YKR072C NEXO1 SOD1 YJR104C NEXO1 XRS2 YDR369C NEXO1 YDJ1 YNL064C NEXO1 YLR352W YLR352W NEXO1 YNL171C YNL171C NEXO1 YPR116W YPR116W N/DHPC2 BUD27 YFL023W NHPC2 CAC2 YML102W YHPC2 CSM3 YMR048W NHPC2 CTF4 YPR135W NHPC2 DDC1 YPL194W N

Page 165: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

HPC2 DOC1 YGL240W NHPC2 ESC2 YDR363W NHPC2 EXO1 YOR033C NHPC2 HPR5 YJL092W NHPC2 HST1 YOL068C NHPC2 HST3 YOR025W NHPC2 LYS7 YMR038C NHPC2 MMS4 YBR098W NHPC2 MRE11 YMR224C NHPC2 MUS81 YDR386W NHPC2 RAD17 YOR368W NHPC2 RAD24 YER173W NHPC2 RAD27 YKL113C YHPC2 RAD50 YNL250W YHPC2 RAD51 YER095W NHPC2 RAD52 YML032C NHPC2 RAD54 YGL163C NHPC2 RAD55 YDR076W NHPC2 RAD57 YDR004W NHPC2 RAD9 YDR217C NHPC2 RPL27A YHR010W NHPC2 RPS30B YOR182C NHPC2 SAE2 YGL175C NHPC2 SGS1 YMR190C NHPC2 SIS2 YKR072C NHPC2 SOD1 YJR104C YHPC2 XRS2 YDR369C NHPC2 YDJ1 YNL064C NHPC2 YLR352W YLR352W NHPC2 YNL171C YNL171C NHPC2 YPR116W YPR116W N/DHPR5 BUD27 YFL023W NHPR5 CAC2 YML102W NHPR5 CSM3 YMR048W YHPR5 CTF4 YPR135W YHPR5 DDC1 YPL194W NHPR5 DOC1 YGL240W NHPR5 ESC2 YDR363W YHPR5 EXO1 YOR033C NHPR5 HPC2 YBR215W NHPR5 HST1 YOL068C NHPR5 HST3 YOR025W NHPR5 LYS7 YMR038C NHPR5 MMS4 YBR098W NHPR5 MRE11 YMR224C NHPR5 MUS81 YDR386W NHPR5 RAD17 YOR368W NHPR5 RAD24 YER173W NHPR5 RAD27 YKL113C YHPR5 RAD50 YNL250W NHPR5 RAD51 YER095W NHPR5 RAD52 YML032C NHPR5 RAD54 YGL163C YHPR5 RAD55 YDR076W NHPR5 RAD57 YDR004W NHPR5 RAD9 YDR217C NHPR5 RPL27A YHR010W NHPR5 RPS30B YOR182C NHPR5 SAE2 YGL175C NHPR5 SGS1 YMR190C YHPR5 SIS2 YKR072C NHPR5 SOD1 YJR104C NHPR5 XRS2 YDR369C YHPR5 YDJ1 YNL064C NHPR5 YLR352W YLR352W NHPR5 YNL171C YNL171C N

Page 166: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

HPR5 YPR116W YPR116W N/DHST1 BUD27 YFL023W NHST1 CAC2 YML102W NHST1 CSM3 YMR048W NHST1 CTF4 YPR135W NHST1 DDC1 YPL194W NHST1 DOC1 YGL240W NHST1 ESC2 YDR363W NHST1 EXO1 YOR033C NHST1 HPC2 YBR215W NHST1 HPR5 YJL092W NHST1 HST3 YOR025W NHST1 LYS7 YMR038C NHST1 MMS4 YBR098W NHST1 MRE11 YMR224C NHST1 MUS81 YDR386W NHST1 RAD17 YOR368W NHST1 RAD24 YER173W NHST1 RAD27 YKL113C YHST1 RAD50 YNL250W NHST1 RAD51 YER095W NHST1 RAD52 YML032C NHST1 RAD54 YGL163C NHST1 RAD55 YDR076W NHST1 RAD57 YDR004W NHST1 RAD9 YDR217C NHST1 RPL27A YHR010W NHST1 RPS30B YOR182C NHST1 SAE2 YGL175C NHST1 SGS1 YMR190C NHST1 SIS2 YKR072C NHST1 SOD1 YJR104C NHST1 XRS2 YDR369C NHST1 YDJ1 YNL064C NHST1 YLR352W YLR352W NHST1 YNL171C YNL171C YHST1 YPR116W YPR116W N/DHST3 BUD27 YFL023W NHST3 CAC2 YML102W NHST3 CSM3 YMR048W YHST3 CTF4 YPR135W NHST3 DDC1 YPL194W NHST3 DOC1 YGL240W NHST3 ESC2 YDR363W NHST3 EXO1 YOR033C YHST3 HPC2 YBR215W NHST3 HPR5 YJL092W NHST3 HST1 YOL068C NHST3 LYS7 YMR038C NHST3 MMS4 YBR098W NHST3 MRE11 YMR224C NHST3 MUS81 YDR386W NHST3 RAD17 YOR368W NHST3 RAD24 YER173W NHST3 RAD27 YKL113C YHST3 RAD50 YNL250W NHST3 RAD51 YER095W NHST3 RAD52 YML032C NHST3 RAD54 YGL163C NHST3 RAD55 YDR076W NHST3 RAD57 YDR004W NHST3 RAD9 YDR217C NHST3 RPL27A YHR010W NHST3 RPS30B YOR182C NHST3 SAE2 YGL175C NHST3 SGS1 YMR190C N

Page 167: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

HST3 SIS2 YKR072C NHST3 SOD1 YJR104C NHST3 XRS2 YDR369C NHST3 YDJ1 YNL064C NHST3 YLR352W YLR352W NHST3 YNL171C YNL171C NHST3 YPR116W YPR116W N/DLYS7 BUD27 YFL023W NLYS7 CAC2 YML102W NLYS7 CSM3 YMR048W YLYS7 CTF4 YPR135W NLYS7 DDC1 YPL194W NLYS7 DOC1 YGL240W NLYS7 ESC2 YDR363W NLYS7 EXO1 YOR033C NLYS7 HPC2 YBR215W NLYS7 HPR5 YJL092W NLYS7 HST1 YOL068C NLYS7 HST3 YOR025W NLYS7 MMS4 YBR098W NLYS7 MRE11 YMR224C YLYS7 MUS81 YDR386W NLYS7 RAD17 YOR368W NLYS7 RAD24 YER173W NLYS7 RAD27 YKL113C YLYS7 RAD50 YNL250W YLYS7 RAD51 YER095W YLYS7 RAD52 YML032C YLYS7 RAD54 YGL163C YLYS7 RAD55 YDR076W N/DLYS7 RAD57 YDR004W NLYS7 RAD9 YDR217C NLYS7 RPL27A YHR010W NLYS7 RPS30B YOR182C NLYS7 SAE2 YGL175C NLYS7 SGS1 YMR190C NLYS7 SIS2 YKR072C NLYS7 SOD1 YJR104C NLYS7 XRS2 YDR369C YLYS7 YDJ1 YNL064C NLYS7 YLR352W YLR352W NLYS7 YNL171C YNL171C NLYS7 YPR116W YPR116W N/DMMS4 BUD27 YFL023W NMMS4 CAC2 YML102W NMMS4 CSM3 YMR048W NMMS4 CTF4 YPR135W NMMS4 DDC1 YPL194W NMMS4 DOC1 YGL240W NMMS4 ESC2 YDR363W YMMS4 EXO1 YOR033C NMMS4 HPC2 YBR215W NMMS4 HPR5 YJL092W NMMS4 HST1 YOL068C NMMS4 HST3 YOR025W NMMS4 LYS7 YMR038C NMMS4 MRE11 YMR224C NMMS4 MUS81 YDR386W NMMS4 RAD17 YOR368W NMMS4 RAD24 YER173W NMMS4 RAD27 YKL113C YMMS4 RAD50 YNL250W NMMS4 RAD51 YER095W NMMS4 RAD52 YML032C NMMS4 RAD54 YGL163C NMMS4 RAD55 YDR076W N

Page 168: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

MMS4 RAD57 YDR004W NMMS4 RAD9 YDR217C NMMS4 RPL27A YHR010W NMMS4 RPS30B YOR182C NMMS4 SAE2 YGL175C NMMS4 SGS1 YMR190C YMMS4 SIS2 YKR072C NMMS4 SOD1 YJR104C NMMS4 XRS2 YDR369C NMMS4 YDJ1 YNL064C NMMS4 YLR352W YLR352W NMMS4 YNL171C YNL171C NMMS4 YPR116W YPR116W N/DMRE11 BUD27 YFL023W NMRE11 CAC2 YML102W YMRE11 CSM3 YMR048W NMRE11 CTF4 YPR135W YMRE11 DDC1 YPL194W NMRE11 DOC1 YGL240W NMRE11 ESC2 YDR363W NMRE11 EXO1 YOR033C YMRE11 HPC2 YBR215W NMRE11 HPR5 YJL092W YMRE11 HST1 YOL068C NMRE11 HST3 YOR025W NMRE11 LYS7 YMR038C YMRE11 MMS4 YBR098W NMRE11 MUS81 YDR386W NMRE11 RAD17 YOR368W NMRE11 RAD24 YER173W NMRE11 RAD27 YKL113C YMRE11 RAD50 YNL250W NMRE11 RAD51 YER095W NMRE11 RAD52 YML032C NMRE11 RAD54 YGL163C NMRE11 RAD55 YDR076W NMRE11 RAD57 YDR004W NMRE11 RAD9 YDR217C NMRE11 RPL27A YHR010W YMRE11 RPS30B YOR182C NMRE11 SAE2 YGL175C NMRE11 SGS1 YMR190C YMRE11 SIS2 YKR072C NMRE11 SOD1 YJR104C YMRE11 XRS2 YDR369C NMRE11 YDJ1 YNL064C YMRE11 YLR352W YLR352W NMRE11 YNL171C YNL171C YMRE11 YPR116W YPR116W N/DMUS81 BUD27 YFL023W NMUS81 CAC2 YML102W NMUS81 CSM3 YMR048W NMUS81 CTF4 YPR135W NMUS81 DDC1 YPL194W NMUS81 DOC1 YGL240W NMUS81 ESC2 YDR363W YMUS81 EXO1 YOR033C NMUS81 HPC2 YBR215W NMUS81 HPR5 YJL092W NMUS81 HST1 YOL068C NMUS81 HST3 YOR025W NMUS81 LYS7 YMR038C YMUS81 MMS4 YBR098W NMUS81 MRE11 YMR224C NMUS81 RAD17 YOR368W NMUS81 RAD24 YER173W N

Page 169: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

MUS81 RAD27 YKL113C YMUS81 RAD50 YNL250W NMUS81 RAD51 YER095W NMUS81 RAD52 YML032C NMUS81 RAD54 YGL163C NMUS81 RAD55 YDR076W NMUS81 RAD57 YDR004W NMUS81 RAD9 YDR217C NMUS81 RPL27A YHR010W NMUS81 RPS30B YOR182C NMUS81 SAE2 YGL175C NMUS81 SGS1 YMR190C YMUS81 SIS2 YKR072C NMUS81 SOD1 YJR104C YMUS81 XRS2 YDR369C YMUS81 YDJ1 YNL064C NMUS81 YLR352W YLR352W NMUS81 YNL171C YNL171C NMUS81 YPR116W YPR116W N/DRAD17 BUD27 YFL023W NRAD17 CAC2 YML102W NRAD17 CSM3 YMR048W NRAD17 CTF4 YPR135W NRAD17 DDC1 YPL194W NRAD17 DOC1 YGL240W NRAD17 ESC2 YDR363W NRAD17 EXO1 YOR033C NRAD17 HPC2 YBR215W NRAD17 HPR5 YJL092W NRAD17 HST1 YOL068C NRAD17 HST3 YOR025W NRAD17 LYS7 YMR038C NRAD17 MMS4 YBR098W NRAD17 MRE11 YMR224C NRAD17 MUS81 YDR386W NRAD17 RAD24 YER173W NRAD17 RAD27 YKL113C YRAD17 RAD50 YNL250W NRAD17 RAD51 YER095W NRAD17 RAD52 YML032C NRAD17 RAD54 YGL163C NRAD17 RAD55 YDR076W NRAD17 RAD57 YDR004W NRAD17 RAD9 YDR217C NRAD17 RPL27A YHR010W NRAD17 RPS30B YOR182C NRAD17 SAE2 YGL175C NRAD17 SGS1 YMR190C NRAD17 SIS2 YKR072C NRAD17 SOD1 YJR104C NRAD17 XRS2 YDR369C NRAD17 YDJ1 YNL064C NRAD17 YLR352W YLR352W NRAD17 YNL171C YNL171C NRAD17 YPR116W YPR116W N/DRAD24 BUD27 YFL023W NRAD24 CAC2 YML102W NRAD24 CSM3 YMR048W NRAD24 CTF4 YPR135W NRAD24 DDC1 YPL194W NRAD24 DOC1 YGL240W NRAD24 ESC2 YDR363W NRAD24 EXO1 YOR033C NRAD24 HPC2 YBR215W NRAD24 HPR5 YJL092W NRAD24 HST1 YOL068C N

Page 170: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

RAD24 HST3 YOR025W NRAD24 LYS7 YMR038C NRAD24 MMS4 YBR098W NRAD24 MRE11 YMR224C NRAD24 MUS81 YDR386W NRAD24 RAD17 YOR368W NRAD24 RAD27 YKL113C YRAD24 RAD50 YNL250W NRAD24 RAD51 YER095W NRAD24 RAD52 YML032C NRAD24 RAD54 YGL163C NRAD24 RAD55 YDR076W NRAD24 RAD57 YDR004W NRAD24 RAD9 YDR217C NRAD24 RPL27A YHR010W NRAD24 RPS30B YOR182C NRAD24 SAE2 YGL175C NRAD24 SGS1 YMR190C NRAD24 SIS2 YKR072C NRAD24 SOD1 YJR104C NRAD24 XRS2 YDR369C NRAD24 YDJ1 YNL064C NRAD24 YLR352W YLR352W NRAD24 YNL171C YNL171C NRAD24 YPR116W YPR116W N/DRAD27 BUD27 YFL023W YRAD27 CAC2 YML102W YRAD27 CSM3 YMR048W YRAD27 CTF4 YPR135W YRAD27 DDC1 YPL194W YRAD27 DOC1 YGL240W YRAD27 ESC2 YDR363W YRAD27 EXO1 YOR033C YRAD27 HPC2 YBR215W YRAD27 HPR5 YJL092W YRAD27 HST1 YOL068C YRAD27 HST3 YOR025W YRAD27 LYS7 YMR038C YRAD27 MMS4 YBR098W YRAD27 MRE11 YMR224C YRAD27 MUS81 YDR386W YRAD27 RAD17 YOR368W YRAD27 RAD24 YER173W YRAD27 RAD50 YNL250W YRAD27 RAD51 YER095W YRAD27 RAD52 YML032C YRAD27 RAD54 YGL163C YRAD27 RAD55 YDR076W YRAD27 RAD57 YDR004W YRAD27 RAD9 YDR217C YRAD27 RPL27A YHR010W YRAD27 RPS30B YOR182C YRAD27 SAE2 YGL175C YRAD27 SGS1 YMR190C YRAD27 SIS2 YKR072C YRAD27 SOD1 YJR104C YRAD27 XRS2 YDR369C YRAD27 YDJ1 YNL064C YRAD27 YLR352W YLR352W YRAD27 YNL171C YNL171C YRAD27 YPR116W YPR116W YRAD50 BUD27 YFL023W NRAD50 CAC2 YML102W YRAD50 CSM3 YMR048W NRAD50 CTF4 YPR135W YRAD50 DDC1 YPL194W N

Page 171: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

RAD50 DOC1 YGL240W NRAD50 ESC2 YDR363W NRAD50 EXO1 YOR033C YRAD50 HPC2 YBR215W YRAD50 HPR5 YJL092W NRAD50 HST1 YOL068C NRAD50 HST3 YOR025W YRAD50 LYS7 YMR038C YRAD50 MMS4 YBR098W NRAD50 MRE11 YMR224C NRAD50 MUS81 YDR386W NRAD50 RAD17 YOR368W YRAD50 RAD24 YER173W NRAD50 RAD27 YKL113C YRAD50 RAD51 YER095W NRAD50 RAD52 YML032C NRAD50 RAD54 YGL163C NRAD50 RAD55 YDR076W YRAD50 RAD57 YDR004W NRAD50 RAD9 YDR217C NRAD50 RPL27A YHR010W YRAD50 RPS30B YOR182C NRAD50 SAE2 YGL175C NRAD50 SGS1 YMR190C YRAD50 SIS2 YKR072C NRAD50 SOD1 YJR104C YRAD50 XRS2 YDR369C NRAD50 YDJ1 YNL064C YRAD50 YLR352W YLR352W NRAD50 YNL171C YNL171C NRAD50 YPR116W YPR116W N/DRAD51 BUD27 YFL023W NRAD51 CAC2 YML102W NRAD51 CSM3 YMR048W NRAD51 CTF4 YPR135W NRAD51 DDC1 YPL194W NRAD51 DOC1 YGL240W NRAD51 ESC2 YDR363W NRAD51 EXO1 YOR033C NRAD51 HPC2 YBR215W NRAD51 HPR5 YJL092W NRAD51 HST1 YOL068C NRAD51 HST3 YOR025W NRAD51 LYS7 YMR038C YRAD51 MMS4 YBR098W NRAD51 MRE11 YMR224C NRAD51 MUS81 YDR386W NRAD51 RAD17 YOR368W NRAD51 RAD24 YER173W NRAD51 RAD27 YKL113C YRAD51 RAD50 YNL250W NRAD51 RAD52 YML032C NRAD51 RAD54 YGL163C NRAD51 RAD55 YDR076W NRAD51 RAD57 YDR004W NRAD51 RAD9 YDR217C NRAD51 RPL27A YHR010W NRAD51 RPS30B YOR182C NRAD51 SAE2 YGL175C NRAD51 SGS1 YMR190C NRAD51 SIS2 YKR072C NRAD51 SOD1 YJR104C YRAD51 XRS2 YDR369C NRAD51 YDJ1 YNL064C NRAD51 YLR352W YLR352W NRAD51 YNL171C YNL171C Y

Page 172: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

RAD51 YPR116W YPR116W N/DRAD52 BUD27 YFL023W NRAD52 CAC2 YML102W NRAD52 CSM3 YMR048W NRAD52 CTF4 YPR135W YRAD52 DDC1 YPL194W NRAD52 DOC1 YGL240W NRAD52 ESC2 YDR363W NRAD52 EXO1 YOR033C NRAD52 HPC2 YBR215W NRAD52 HPR5 YJL092W NRAD52 HST1 YOL068C NRAD52 HST3 YOR025W NRAD52 LYS7 YMR038C YRAD52 MMS4 YBR098W NRAD52 MRE11 YMR224C NRAD52 MUS81 YDR386W NRAD52 RAD17 YOR368W NRAD52 RAD24 YER173W NRAD52 RAD27 YKL113C YRAD52 RAD50 YNL250W NRAD52 RAD51 YER095W NRAD52 RAD54 YGL163C NRAD52 RAD55 YDR076W NRAD52 RAD57 YDR004W NRAD52 RAD9 YDR217C NRAD52 RPL27A YHR010W YRAD52 RPS30B YOR182C NRAD52 SAE2 YGL175C NRAD52 SGS1 YMR190C NRAD52 SIS2 YKR072C NRAD52 SOD1 YJR104C YRAD52 XRS2 YDR369C NRAD52 YDJ1 YNL064C NRAD52 YLR352W YLR352W NRAD52 YNL171C YNL171C YRAD52 YPR116W YPR116W N/DRAD54 BUD27 YFL023W N/DRAD54 CAC2 YML102W N/DRAD54 CSM3 YMR048W N/DRAD54 CTF4 YPR135W N/DRAD54 DDC1 YPL194W N/DRAD54 DOC1 YGL240W N/DRAD54 ESC2 YDR363W N/DRAD54 EXO1 YOR033C N/DRAD54 HPC2 YBR215W N/DRAD54 HPR5 YJL092W N/DRAD54 HST1 YOL068C N/DRAD54 HST3 YOR025W N/DRAD54 LYS7 YMR038C N/DRAD54 MMS4 YBR098W N/DRAD54 MRE11 YMR224C N/DRAD54 MUS81 YDR386W N/DRAD54 RAD17 YOR368W N/DRAD54 RAD24 YER173W N/DRAD54 RAD27 YKL113C N/DRAD54 RAD50 YNL250W N/DRAD54 RAD51 YER095W N/DRAD54 RAD52 YML032C N/DRAD54 RAD55 YDR076W N/DRAD54 RAD57 YDR004W N/DRAD54 RAD9 YDR217C N/DRAD54 RPL27A YHR010W N/DRAD54 RPS30B YOR182C N/DRAD54 SAE2 YGL175C N/DRAD54 SGS1 YMR190C N/D

Page 173: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

RAD54 SIS2 YKR072C N/DRAD54 SOD1 YJR104C N/DRAD54 XRS2 YDR369C N/DRAD54 YDJ1 YNL064C N/DRAD54 YLR352W YLR352W N/DRAD54 YNL171C YNL171C N/DRAD54 YPR116W YPR116W N/DRAD55 BUD27 YFL023W N/DRAD55 CAC2 YML102W N/DRAD55 CSM3 YMR048W N/DRAD55 CTF4 YPR135W N/DRAD55 DDC1 YPL194W N/DRAD55 DOC1 YGL240W N/DRAD55 ESC2 YDR363W N/DRAD55 EXO1 YOR033C N/DRAD55 HPC2 YBR215W N/DRAD55 HPR5 YJL092W N/DRAD55 HST1 YOL068C N/DRAD55 HST3 YOR025W N/DRAD55 LYS7 YMR038C N/DRAD55 MMS4 YBR098W N/DRAD55 MRE11 YMR224C N/DRAD55 MUS81 YDR386W N/DRAD55 RAD17 YOR368W N/DRAD55 RAD24 YER173W N/DRAD55 RAD27 YKL113C N/DRAD55 RAD50 YNL250W N/DRAD55 RAD51 YER095W N/DRAD55 RAD52 YML032C N/DRAD55 RAD54 YGL163C N/DRAD55 RAD57 YDR004W N/DRAD55 RAD9 YDR217C N/DRAD55 RPL27A YHR010W N/DRAD55 RPS30B YOR182C N/DRAD55 SAE2 YGL175C N/DRAD55 SGS1 YMR190C N/DRAD55 SIS2 YKR072C N/DRAD55 SOD1 YJR104C N/DRAD55 XRS2 YDR369C N/DRAD55 YDJ1 YNL064C N/DRAD55 YLR352W YLR352W N/DRAD55 YNL171C YNL171C N/DRAD55 YPR116W YPR116W N/DRAD57 BUD27 YFL023W NRAD57 CAC2 YML102W NRAD57 CSM3 YMR048W NRAD57 CTF4 YPR135W NRAD57 DDC1 YPL194W NRAD57 DOC1 YGL240W NRAD57 ESC2 YDR363W NRAD57 EXO1 YOR033C NRAD57 HPC2 YBR215W NRAD57 HPR5 YJL092W NRAD57 HST1 YOL068C NRAD57 HST3 YOR025W NRAD57 LYS7 YMR038C YRAD57 MMS4 YBR098W NRAD57 MRE11 YMR224C NRAD57 MUS81 YDR386W NRAD57 RAD17 YOR368W NRAD57 RAD24 YER173W NRAD57 RAD27 YKL113C YRAD57 RAD50 YNL250W NRAD57 RAD51 YER095W NRAD57 RAD52 YML032C NRAD57 RAD54 YGL163C N

Page 174: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

RAD57 RAD55 YDR076W NRAD57 RAD9 YDR217C NRAD57 RPL27A YHR010W NRAD57 RPS30B YOR182C NRAD57 SAE2 YGL175C NRAD57 SGS1 YMR190C NRAD57 SIS2 YKR072C NRAD57 SOD1 YJR104C NRAD57 XRS2 YDR369C NRAD57 YDJ1 YNL064C NRAD57 YLR352W YLR352W NRAD57 YNL171C YNL171C NRAD57 YPR116W YPR116W N/DRAD9 BUD27 YFL023W NRAD9 CAC2 YML102W NRAD9 CSM3 YMR048W YRAD9 CTF4 YPR135W NRAD9 DDC1 YPL194W NRAD9 DOC1 YGL240W NRAD9 ESC2 YDR363W NRAD9 EXO1 YOR033C NRAD9 HPC2 YBR215W NRAD9 HPR5 YJL092W NRAD9 HST1 YOL068C NRAD9 HST3 YOR025W NRAD9 LYS7 YMR038C NRAD9 MMS4 YBR098W NRAD9 MRE11 YMR224C NRAD9 MUS81 YDR386W NRAD9 RAD17 YOR368W NRAD9 RAD24 YER173W NRAD9 RAD27 YKL113C YRAD9 RAD50 YNL250W NRAD9 RAD51 YER095W NRAD9 RAD52 YML032C NRAD9 RAD54 YGL163C NRAD9 RAD55 YDR076W NRAD9 RAD57 YDR004W NRAD9 RPL27A YHR010W NRAD9 RPS30B YOR182C NRAD9 SAE2 YGL175C NRAD9 SGS1 YMR190C NRAD9 SIS2 YKR072C NRAD9 SOD1 YJR104C NRAD9 XRS2 YDR369C NRAD9 YDJ1 YNL064C NRAD9 YLR352W YLR352W NRAD9 YNL171C YNL171C NRAD9 YPR116W YPR116W N/DRPL27A BUD27 YFL023W NRPL27A CAC2 YML102W NRPL27A CSM3 YMR048W NRPL27A CTF4 YPR135W YRPL27A DDC1 YPL194W NRPL27A DOC1 YGL240W NRPL27A ESC2 YDR363W NRPL27A EXO1 YOR033C NRPL27A HPC2 YBR215W YRPL27A HPR5 YJL092W NRPL27A HST1 YOL068C NRPL27A HST3 YOR025W NRPL27A LYS7 YMR038C NRPL27A MMS4 YBR098W NRPL27A MRE11 YMR224C YRPL27A MUS81 YDR386W NRPL27A RAD17 YOR368W N

Page 175: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

RPL27A RAD24 YER173W NRPL27A RAD27 YKL113C YRPL27A RAD50 YNL250W YRPL27A RAD51 YER095W NRPL27A RAD52 YML032C YRPL27A RAD54 YGL163C NRPL27A RAD55 YDR076W NRPL27A RAD57 YDR004W NRPL27A RAD9 YDR217C NRPL27A RPS30B YOR182C NRPL27A SAE2 YGL175C NRPL27A SGS1 YMR190C YRPL27A SIS2 YKR072C NRPL27A SOD1 YJR104C YRPL27A XRS2 YDR369C NRPL27A YDJ1 YNL064C NRPL27A YLR352W YLR352W NRPL27A YNL171C YNL171C YRPL27A YPR116W YPR116W N/DRPS30B BUD27 YFL023W NRPS30B CAC2 YML102W NRPS30B CSM3 YMR048W NRPS30B CTF4 YPR135W NRPS30B DDC1 YPL194W NRPS30B DOC1 YGL240W NRPS30B ESC2 YDR363W NRPS30B EXO1 YOR033C NRPS30B HPC2 YBR215W NRPS30B HPR5 YJL092W NRPS30B HST1 YOL068C NRPS30B HST3 YOR025W NRPS30B LYS7 YMR038C NRPS30B MMS4 YBR098W NRPS30B MRE11 YMR224C NRPS30B MUS81 YDR386W NRPS30B RAD17 YOR368W NRPS30B RAD24 YER173W NRPS30B RAD27 YKL113C YRPS30B RAD50 YNL250W NRPS30B RAD51 YER095W NRPS30B RAD52 YML032C NRPS30B RAD54 YGL163C NRPS30B RAD55 YDR076W NRPS30B RAD57 YDR004W NRPS30B RAD9 YDR217C NRPS30B RPL27A YHR010W NRPS30B SAE2 YGL175C NRPS30B SGS1 YMR190C NRPS30B SIS2 YKR072C NRPS30B SOD1 YJR104C NRPS30B XRS2 YDR369C NRPS30B YDJ1 YNL064C NRPS30B YLR352W YLR352W NRPS30B YNL171C YNL171C YRPS30B YPR116W YPR116W N/DSAE2 BUD27 YFL023W NSAE2 CAC2 YML102W NSAE2 CSM3 YMR048W NSAE2 CTF4 YPR135W NSAE2 DDC1 YPL194W NSAE2 DOC1 YGL240W NSAE2 ESC2 YDR363W NSAE2 EXO1 YOR033C NSAE2 HPC2 YBR215W NSAE2 HPR5 YJL092W NSAE2 HST1 YOL068C N

Page 176: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

SAE2 HST3 YOR025W NSAE2 LYS7 YMR038C NSAE2 MMS4 YBR098W NSAE2 MRE11 YMR224C NSAE2 MUS81 YDR386W NSAE2 RAD17 YOR368W NSAE2 RAD24 YER173W NSAE2 RAD27 YKL113C YSAE2 RAD50 YNL250W NSAE2 RAD51 YER095W NSAE2 RAD52 YML032C NSAE2 RAD54 YGL163C YSAE2 RAD55 YDR076W NSAE2 RAD57 YDR004W NSAE2 RAD9 YDR217C NSAE2 RPL27A YHR010W NSAE2 RPS30B YOR182C NSAE2 SGS1 YMR190C YSAE2 SIS2 YKR072C NSAE2 SOD1 YJR104C NSAE2 XRS2 YDR369C NSAE2 YDJ1 YNL064C NSAE2 YLR352W YLR352W NSAE2 YNL171C YNL171C NSAE2 YPR116W YPR116W N/DSGS1 BUD27 YFL023W NSGS1 CAC2 YML102W NSGS1 CSM3 YMR048W YSGS1 CTF4 YPR135W NSGS1 DDC1 YPL194W NSGS1 DOC1 YGL240W NSGS1 ESC2 YDR363W YSGS1 EXO1 YOR033C NSGS1 HPC2 YBR215W NSGS1 HPR5 YJL092W YSGS1 HST1 YOL068C NSGS1 HST3 YOR025W NSGS1 LYS7 YMR038C NSGS1 MMS4 YBR098W YSGS1 MRE11 YMR224C NSGS1 MUS81 YDR386W YSGS1 RAD17 YOR368W NSGS1 RAD24 YER173W NSGS1 RAD27 YKL113C YSGS1 RAD50 YNL250W YSGS1 RAD51 YER095W NSGS1 RAD52 YML032C NSGS1 RAD54 YGL163C NSGS1 RAD55 YDR076W NSGS1 RAD57 YDR004W NSGS1 RAD9 YDR217C NSGS1 RPL27A YHR010W NSGS1 RPS30B YOR182C NSGS1 SAE2 YGL175C YSGS1 SIS2 YKR072C YSGS1 SOD1 YJR104C NSGS1 XRS2 YDR369C NSGS1 YDJ1 YNL064C NSGS1 YLR352W YLR352W NSGS1 YNL171C YNL171C NSGS1 YPR116W YPR116W NSIS2 BUD27 YFL023W NSIS2 CAC2 YML102W NSIS2 CSM3 YMR048W NSIS2 CTF4 YPR135W NSIS2 DDC1 YPL194W N

Page 177: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

SIS2 DOC1 YGL240W NSIS2 ESC2 YDR363W NSIS2 EXO1 YOR033C NSIS2 HPC2 YBR215W NSIS2 HPR5 YJL092W NSIS2 HST1 YOL068C NSIS2 HST3 YOR025W NSIS2 LYS7 YMR038C NSIS2 MMS4 YBR098W NSIS2 MRE11 YMR224C NSIS2 MUS81 YDR386W NSIS2 RAD17 YOR368W NSIS2 RAD24 YER173W NSIS2 RAD27 YKL113C YSIS2 RAD50 YNL250W NSIS2 RAD51 YER095W NSIS2 RAD52 YML032C NSIS2 RAD54 YGL163C NSIS2 RAD55 YDR076W NSIS2 RAD57 YDR004W NSIS2 RAD9 YDR217C NSIS2 RPL27A YHR010W NSIS2 RPS30B YOR182C NSIS2 SAE2 YGL175C NSIS2 SGS1 YMR190C YSIS2 SOD1 YJR104C YSIS2 XRS2 YDR369C NSIS2 YDJ1 YNL064C NSIS2 YLR352W YLR352W NSIS2 YNL171C YNL171C NSIS2 YPR116W YPR116W N/DSOD1 BUD27 YFL023W YSOD1 CAC2 YML102W NSOD1 CSM3 YMR048W NSOD1 CTF4 YPR135W NSOD1 DDC1 YPL194W NSOD1 DOC1 YGL240W NSOD1 ESC2 YDR363W NSOD1 EXO1 YOR033C NSOD1 HPC2 YBR215W NSOD1 HPR5 YJL092W NSOD1 HST1 YOL068C NSOD1 HST3 YOR025W NSOD1 LYS7 YMR038C NSOD1 MMS4 YBR098W NSOD1 MRE11 YMR224C YSOD1 MUS81 YDR386W NSOD1 RAD17 YOR368W NSOD1 RAD24 YER173W NSOD1 RAD27 YKL113C YSOD1 RAD50 YNL250W YSOD1 RAD51 YER095W YSOD1 RAD52 YML032C YSOD1 RAD54 YGL163C YSOD1 RAD55 YDR076W YSOD1 RAD57 YDR004W NSOD1 RAD9 YDR217C NSOD1 RPL27A YHR010W YSOD1 RPS30B YOR182C NSOD1 SAE2 YGL175C NSOD1 SGS1 YMR190C YSOD1 SIS2 YKR072C NSOD1 XRS2 YDR369C NSOD1 YDJ1 YNL064C NSOD1 YLR352W YLR352W NSOD1 YNL171C YNL171C Y

Page 178: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

SOD1 YPR116W YPR116W N/DXRS2 BUD27 YFL023W NXRS2 CAC2 YML102W YXRS2 CSM3 YMR048W NXRS2 CTF4 YPR135W YXRS2 DDC1 YPL194W NXRS2 DOC1 YGL240W NXRS2 ESC2 YDR363W YXRS2 EXO1 YOR033C YXRS2 HPC2 YBR215W NXRS2 HPR5 YJL092W YXRS2 HST1 YOL068C NXRS2 HST3 YOR025W NXRS2 LYS7 YMR038C YXRS2 MMS4 YBR098W NXRS2 MRE11 YMR224C NXRS2 MUS81 YDR386W YXRS2 RAD17 YOR368W NXRS2 RAD24 YER173W NXRS2 RAD27 YKL113C YXRS2 RAD50 YNL250W NXRS2 RAD51 YER095W NXRS2 RAD52 YML032C NXRS2 RAD54 YGL163C NXRS2 RAD55 YDR076W NXRS2 RAD57 YDR004W NXRS2 RAD9 YDR217C NXRS2 RPL27A YHR010W NXRS2 RPS30B YOR182C YXRS2 SAE2 YGL175C NXRS2 SGS1 YMR190C NXRS2 SIS2 YKR072C NXRS2 SOD1 YJR104C YXRS2 YDJ1 YNL064C YXRS2 YLR352W YLR352W NXRS2 YNL171C YNL171C YXRS2 YPR116W YPR116W N/DYDJ1 BUD27 YFL023W YYDJ1 CAC2 YML102W NYDJ1 CSM3 YMR048W NYDJ1 CTF4 YPR135W NYDJ1 DDC1 YPL194W NYDJ1 DOC1 YGL240W NYDJ1 ESC2 YDR363W NYDJ1 EXO1 YOR033C NYDJ1 HPC2 YBR215W NYDJ1 HPR5 YJL092W NYDJ1 HST1 YOL068C NYDJ1 HST3 YOR025W NYDJ1 LYS7 YMR038C NYDJ1 MMS4 YBR098W NYDJ1 MRE11 YMR224C YYDJ1 MUS81 YDR386W NYDJ1 RAD17 YOR368W NYDJ1 RAD24 YER173W NYDJ1 RAD27 YKL113C YYDJ1 RAD50 YNL250W YYDJ1 RAD51 YER095W NYDJ1 RAD52 YML032C YYDJ1 RAD54 YGL163C NYDJ1 RAD55 YDR076W NYDJ1 RAD57 YDR004W NYDJ1 RAD9 YDR217C NYDJ1 RPL27A YHR010W NYDJ1 RPS30B YOR182C NYDJ1 SAE2 YGL175C N

Page 179: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

YDJ1 SGS1 YMR190C NYDJ1 SIS2 YKR072C NYDJ1 SOD1 YJR104C YYDJ1 XRS2 YDR369C NYDJ1 YLR352W YLR352W NYDJ1 YNL171C YNL171C YYDJ1 YPR116W YPR116W N/DYLR352W BUD27 YFL023W NYLR352W CAC2 YML102W NYLR352W CSM3 YMR048W NYLR352W CTF4 YPR135W NYLR352W DDC1 YPL194W NYLR352W DOC1 YGL240W NYLR352W ESC2 YDR363W NYLR352W EXO1 YOR033C NYLR352W HPC2 YBR215W NYLR352W HPR5 YJL092W NYLR352W HST1 YOL068C NYLR352W HST3 YOR025W NYLR352W LYS7 YMR038C NYLR352W MMS4 YBR098W NYLR352W MRE11 YMR224C NYLR352W MUS81 YDR386W NYLR352W RAD17 YOR368W NYLR352W RAD24 YER173W NYLR352W RAD27 YKL113C YYLR352W RAD50 YNL250W NYLR352W RAD51 YER095W NYLR352W RAD52 YML032C NYLR352W RAD54 YGL163C NYLR352W RAD55 YDR076W NYLR352W RAD57 YDR004W NYLR352W RAD9 YDR217C NYLR352W RPL27A YHR010W NYLR352W RPS30B YOR182C NYLR352W SAE2 YGL175C NYLR352W SGS1 YMR190C NYLR352W SIS2 YKR072C NYLR352W SOD1 YJR104C NYLR352W XRS2 YDR369C NYLR352W YDJ1 YNL064C NYLR352W YNL171C YNL171C NYLR352W YPR116W YPR116W N/DYNL171C BUD27 YFL023W NYNL171C CAC2 YML102W YYNL171C CSM3 YMR048W NYNL171C CTF4 YPR135W NYNL171C DDC1 YPL194W NYNL171C DOC1 YGL240W NYNL171C ESC2 YDR363W NYNL171C EXO1 YOR033C NYNL171C HPC2 YBR215W NYNL171C HPR5 YJL092W NYNL171C HST1 YOL068C NYNL171C HST3 YOR025W NYNL171C LYS7 YMR038C NYNL171C MMS4 YBR098W NYNL171C MRE11 YMR224C YYNL171C MUS81 YDR386W NYNL171C RAD17 YOR368W NYNL171C RAD24 YER173W NYNL171C RAD27 YKL113C YYNL171C RAD50 YNL250W NYNL171C RAD51 YER095W NYNL171C RAD52 YML032C NYNL171C RAD54 YGL163C N

Page 180: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

YNL171C RAD55 YDR076W NYNL171C RAD57 YDR004W NYNL171C RAD9 YDR217C NYNL171C RPL27A YHR010W NYNL171C RPS30B YOR182C NYNL171C SAE2 YGL175C NYNL171C SGS1 YMR190C NYNL171C SIS2 YKR072C NYNL171C SOD1 YJR104C NYNL171C XRS2 YDR369C NYNL171C YDJ1 YNL064C NYNL171C YLR352W YLR352W NYNL171C YPR116W YPR116W N/DYPR116W BUD27 YFL023W NYPR116W CAC2 YML102W NYPR116W CSM3 YMR048W NYPR116W CTF4 YPR135W YYPR116W DDC1 YPL194W NYPR116W DOC1 YGL240W NYPR116W ESC2 YDR363W NYPR116W EXO1 YOR033C NYPR116W HPC2 YBR215W NYPR116W HPR5 YJL092W NYPR116W HST1 YOL068C NYPR116W HST3 YOR025W NYPR116W LYS7 YMR038C NYPR116W MMS4 YBR098W NYPR116W MRE11 YMR224C NYPR116W MUS81 YDR386W NYPR116W RAD17 YOR368W NYPR116W RAD24 YER173W NYPR116W RAD27 YKL113C YYPR116W RAD50 YNL250W NYPR116W RAD51 YER095W NYPR116W RAD52 YML032C NYPR116W RAD54 YGL163C NYPR116W RAD55 YDR076W NYPR116W RAD57 YDR004W NYPR116W RAD9 YDR217C NYPR116W RPL27A YHR010W NYPR116W RPS30B YOR182C NYPR116W SAE2 YGL175C NYPR116W SGS1 YMR190C NYPR116W SIS2 YKR072C NYPR116W SOD1 YJR104C NYPR116W XRS2 YDR369C NYPR116W YDJ1 YNL064C NYPR116W YLR352W YLR352W NYPR116W YNL171C YNL171C NASF1 CSM3 YMR048W NASF1 ESC2 YDR363W NASF1 HPR5 YJL092W NASF1 MGS1 YNL218W NASF1 MMS4 YBR098W NASF1 MUS81 YDR386W NASF1 POL32 YJR043C NASF1 PUB1 YNL016W NASF1 RAD27 YKL113C YASF1 RAD50 YNL250W NASF1 RNR1 YER070W N/DASF1 RPL24A YGL031C NASF1 RRM3 YHR031C NASF1 RTT107 YHR154W NASF1 SAE2 YGL175C NASF1 SGS1 YMR190C YASF1 SIS2 YKR072C N

Page 181: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

ASF1 SLX1 YBR228W NASF1 SLX4 YLR135W NASF1 SOD1 YJR104C NASF1 SWE1 YJL187C NASF1 TOP1 YOL006C NASF1 WSS1 YHR134W NASF1 YBR094W YBR094W NCSM3 ASF1 YJL115W NCSM3 ESC2 YDR363W NCSM3 HPR5 YJL092W YCSM3 MGS1 YNL218W NCSM3 MMS4 YBR098W NCSM3 MUS81 YDR386W NCSM3 POL32 YJR043C YCSM3 PUB1 YNL016W NCSM3 RAD27 YKL113C YCSM3 RAD50 YNL250W NCSM3 RNR1 YER070W N/DCSM3 RPL24A YGL031C NCSM3 RRM3 YHR031C NCSM3 RTT107 YHR154W NCSM3 SAE2 YGL175C NCSM3 SGS1 YMR190C YCSM3 SIS2 YKR072C NCSM3 SLX1 YBR228W NCSM3 SLX4 YLR135W NCSM3 SOD1 YJR104C NCSM3 SWE1 YJL187C NCSM3 TOP1 YOL006C NCSM3 WSS1 YHR134W NCSM3 YBR094W YBR094W NESC2 ASF1 YJL115W NESC2 CSM3 YMR048W NESC2 HPR5 YJL092W YESC2 MGS1 YNL218W YESC2 MMS4 YBR098W YESC2 MUS81 YDR386W YESC2 POL32 YJR043C NESC2 PUB1 YNL016W NESC2 RAD27 YKL113C YESC2 RAD50 YNL250W NESC2 RNR1 YER070W N/DESC2 RPL24A YGL031C NESC2 RRM3 YHR031C YESC2 RTT107 YHR154W NESC2 SAE2 YGL175C NESC2 SGS1 YMR190C YESC2 SIS2 YKR072C NESC2 SLX1 YBR228W YESC2 SLX4 YLR135W YESC2 SOD1 YJR104C NESC2 SWE1 YJL187C NESC2 TOP1 YOL006C NESC2 WSS1 YHR134W YESC2 YBR094W YBR094W YHPR5 ASF1 YJL115W YHPR5 CSM3 YMR048W YHPR5 ESC2 YDR363W YHPR5 MGS1 YNL218W NHPR5 MMS4 YBR098W NHPR5 MUS81 YDR386W NHPR5 POL32 YJR043C YHPR5 PUB1 YNL016W NHPR5 RAD27 YKL113C YHPR5 RAD50 YNL250W NHPR5 RNR1 YER070W N/D

Page 182: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

HPR5 RPL24A YGL031C NHPR5 RRM3 YHR031C YHPR5 RTT107 YHR154W NHPR5 SAE2 YGL175C NHPR5 SGS1 YMR190C YHPR5 SIS2 YKR072C NHPR5 SLX1 YBR228W NHPR5 SLX4 YLR135W NHPR5 SOD1 YJR104C NHPR5 SWE1 YJL187C NHPR5 TOP1 YOL006C NHPR5 WSS1 YHR134W NHPR5 YBR094W YBR094W NMGS1 ASF1 YJL115W NMGS1 CSM3 YMR048W NMGS1 ESC2 YDR363W YMGS1 HPR5 YJL092W NMGS1 MMS4 YBR098W NMGS1 MUS81 YDR386W NMGS1 POL32 YJR043C NMGS1 PUB1 YNL016W NMGS1 RAD27 YKL113C NMGS1 RAD50 YNL250W YMGS1 RNR1 YER070W N/DMGS1 RPL24A YGL031C NMGS1 RRM3 YHR031C NMGS1 RTT107 YHR154W NMGS1 SAE2 YGL175C NMGS1 SGS1 YMR190C YMGS1 SIS2 YKR072C NMGS1 SLX1 YBR228W NMGS1 SLX4 YLR135W NMGS1 SOD1 YJR104C NMGS1 SWE1 YJL187C NMGS1 TOP1 YOL006C NMGS1 WSS1 YHR134W NMGS1 YBR094W YBR094W NMMS4 ASF1 YJL115W YMMS4 CSM3 YMR048W NMMS4 ESC2 YDR363W YMMS4 HPR5 YJL092W NMMS4 MGS1 YNL218W NMMS4 MUS81 YDR386W NMMS4 POL32 YJR043C YMMS4 PUB1 YNL016W NMMS4 RAD27 YKL113C YMMS4 RAD50 YNL250W NMMS4 RNR1 YER070W N/DMMS4 RPL24A YGL031C NMMS4 RRM3 YHR031C NMMS4 RTT107 YHR154W NMMS4 SAE2 YGL175C NMMS4 SGS1 YMR190C YMMS4 SIS2 YKR072C NMMS4 SLX1 YBR228W NMMS4 SLX4 YLR135W NMMS4 SOD1 YJR104C NMMS4 SWE1 YJL187C NMMS4 TOP1 YOL006C NMMS4 WSS1 YHR134W NMMS4 YBR094W YBR094W YMUS81 ASF1 YJL115W NMUS81 CSM3 YMR048W NMUS81 ESC2 YDR363W YMUS81 HPR5 YJL092W NMUS81 MGS1 YNL218W N

Page 183: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

MUS81 MMS4 YBR098W NMUS81 POL32 YJR043C YMUS81 PUB1 YNL016W NMUS81 RAD27 YKL113C YMUS81 RAD50 YNL250W NMUS81 RNR1 YER070W N/DMUS81 RPL24A YGL031C NMUS81 RRM3 YHR031C NMUS81 RTT107 YHR154W NMUS81 SAE2 YGL175C NMUS81 SGS1 YMR190C YMUS81 SIS2 YKR072C NMUS81 SLX1 YBR228W NMUS81 SLX4 YLR135W NMUS81 SOD1 YJR104C YMUS81 SWE1 YJL187C NMUS81 TOP1 YOL006C NMUS81 WSS1 YHR134W NMUS81 YBR094W YBR094W NPOL32 ASF1 YJL115W NPOL32 CSM3 YMR048W YPOL32 ESC2 YDR363W YPOL32 HPR5 YJL092W YPOL32 MGS1 YNL218W NPOL32 MMS4 YBR098W YPOL32 MUS81 YDR386W NPOL32 PUB1 YNL016W NPOL32 RAD27 YKL113C YPOL32 RAD50 YNL250W YPOL32 RNR1 YER070W N/DPOL32 RPL24A YGL031C NPOL32 RRM3 YHR031C NPOL32 RTT107 YHR154W NPOL32 SAE2 YGL175C NPOL32 SGS1 YMR190C YPOL32 SIS2 YKR072C NPOL32 SLX1 YBR228W NPOL32 SLX4 YLR135W NPOL32 SOD1 YJR104C YPOL32 SWE1 YJL187C NPOL32 TOP1 YOL006C NPOL32 WSS1 YHR134W NPOL32 YBR094W YBR094W YPUB1 ASF1 YJL115W NPUB1 CSM3 YMR048W NPUB1 ESC2 YDR363W NPUB1 HPR5 YJL092W NPUB1 MGS1 YNL218W NPUB1 MMS4 YBR098W NPUB1 MUS81 YDR386W NPUB1 POL32 YJR043C NPUB1 RAD27 YKL113C NPUB1 RAD50 YNL250W NPUB1 RNR1 YER070W N/DPUB1 RPL24A YGL031C NPUB1 RRM3 YHR031C NPUB1 RTT107 YHR154W NPUB1 SAE2 YGL175C NPUB1 SGS1 YMR190C YPUB1 SIS2 YKR072C NPUB1 SLX1 YBR228W NPUB1 SLX4 YLR135W NPUB1 SOD1 YJR104C NPUB1 SWE1 YJL187C NPUB1 TOP1 YOL006C NPUB1 WSS1 YHR134W N

Page 184: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

PUB1 YBR094W YBR094W NRAD27 ASF1 YJL115W NRAD27 CSM3 YMR048W YRAD27 ESC2 YDR363W YRAD27 HPR5 YJL092W YRAD27 MGS1 YNL218W NRAD27 MMS4 YBR098W YRAD27 MUS81 YDR386W YRAD27 POL32 YJR043C NRAD27 PUB1 YNL016W NRAD27 RAD27 YKL113C NRAD27 RAD50 YNL250W YRAD27 RNR1 YER070W NRAD27 RPL24A YGL031C NRAD27 RRM3 YHR031C NRAD27 RTT107 YHR154W NRAD27 SAE2 YGL175C YRAD27 SGS1 YMR190C YRAD27 SIS2 YKR072C YRAD27 SLX1 YBR228W NRAD27 SLX4 YLR135W NRAD27 SOD1 YJR104C YRAD27 SWE1 YJL187C NRAD27 TOP1 YOL006C NRAD27 WSS1 YHR134W NRAD50 ASF1 YJL115W YRAD50 CSM3 YMR048W NRAD50 ESC2 YDR363W NRAD50 HPR5 YJL092W NRAD50 MGS1 YNL218W YRAD50 MMS4 YBR098W NRAD50 MUS81 YDR386W NRAD50 POL32 YJR043C YRAD50 PUB1 YNL016W NRAD50 RAD27 YKL113C YRAD50 RNR1 YER070W N/DRAD50 RPL24A YGL031C NRAD50 RRM3 YHR031C YRAD50 RTT107 YHR154W YRAD50 SAE2 YGL175C NRAD50 SGS1 YMR190C YRAD50 SIS2 YKR072C NRAD50 SLX1 YBR228W NRAD50 SLX4 YLR135W YRAD50 SOD1 YJR104C YRAD50 SWE1 YJL187C NRAD50 TOP1 YOL006C YRAD50 WSS1 YHR134W YRAD50 YBR094W YBR094W NRNR1 ASF1 YJL115W NRNR1 CSM3 YMR048W YRNR1 ESC2 YDR363W YRNR1 HPR5 YJL092W NRNR1 MGS1 YNL218W NRNR1 MMS4 YBR098W NRNR1 MUS81 YDR386W NRNR1 POL32 YJR043C NRNR1 PUB1 YNL016W NRNR1 RAD27 YKL113C NRNR1 RAD50 YNL250W NRNR1 RPL24A YGL031C NRNR1 RRM3 YHR031C NRNR1 RTT107 YHR154W NRNR1 SAE2 YGL175C NRNR1 SGS1 YMR190C YRNR1 SIS2 YKR072C N

Page 185: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

RNR1 SLX1 YBR228W NRNR1 SLX4 YLR135W NRNR1 SOD1 YJR104C N/DRNR1 SWE1 YJL187C NRNR1 TOP1 YOL006C NRNR1 WSS1 YHR134W NRNR1 YBR094W YBR094W NRPL24A ASF1 YJL115W NRPL24A CSM3 YMR048W NRPL24A ESC2 YDR363W NRPL24A HPR5 YJL092W NRPL24A MGS1 YNL218W NRPL24A MMS4 YBR098W NRPL24A MUS81 YDR386W NRPL24A POL32 YJR043C NRPL24A PUB1 YNL016W NRPL24A RAD27 YKL113C NRPL24A RAD50 YNL250W NRPL24A RNR1 YER070W N/DRPL24A RRM3 YHR031C NRPL24A RTT107 YHR154W NRPL24A SAE2 YGL175C NRPL24A SGS1 YMR190C YRPL24A SIS2 YKR072C NRPL24A SLX1 YBR228W NRPL24A SLX4 YLR135W NRPL24A SOD1 YJR104C NRPL24A SWE1 YJL187C NRPL24A TOP1 YOL006C NRPL24A WSS1 YHR134W NRPL24A YBR094W YBR094W NRRM3 ASF1 YJL115W YRRM3 CSM3 YMR048W NRRM3 ESC2 YDR363W YRRM3 HPR5 YJL092W YRRM3 MGS1 YNL218W NRRM3 MMS4 YBR098W NRRM3 MUS81 YDR386W NRRM3 POL32 YJR043C NRRM3 PUB1 YNL016W NRRM3 RAD27 YKL113C NRRM3 RAD50 YNL250W YRRM3 RNR1 YER070W N/DRRM3 RPL24A YGL031C NRRM3 RTT107 YHR154W YRRM3 SAE2 YGL175C NRRM3 SGS1 YMR190C YRRM3 SIS2 YKR072C NRRM3 SLX1 YBR228W NRRM3 SLX4 YLR135W NRRM3 SOD1 YJR104C NRRM3 SWE1 YJL187C NRRM3 TOP1 YOL006C NRRM3 WSS1 YHR134W NRRM3 YBR094W YBR094W NRTT107 ASF1 YJL115W NRTT107 CSM3 YMR048W NRTT107 ESC2 YDR363W NRTT107 HPR5 YJL092W NRTT107 MGS1 YNL218W NRTT107 MMS4 YBR098W NRTT107 MUS81 YDR386W NRTT107 POL32 YJR043C NRTT107 PUB1 YNL016W NRTT107 RAD27 YKL113C NRTT107 RAD50 YNL250W N

Page 186: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

RTT107 RNR1 YER070W N/DRTT107 RPL24A YGL031C NRTT107 RRM3 YHR031C YRTT107 SAE2 YGL175C NRTT107 SGS1 YMR190C YRTT107 SIS2 YKR072C NRTT107 SLX1 YBR228W NRTT107 SLX4 YLR135W NRTT107 SOD1 YJR104C YRTT107 SWE1 YJL187C NRTT107 TOP1 YOL006C NRTT107 WSS1 YHR134W YRTT107 YBR094W YBR094W NSAE2 ASF1 YJL115W NSAE2 CSM3 YMR048W NSAE2 ESC2 YDR363W NSAE2 HPR5 YJL092W NSAE2 MGS1 YNL218W NSAE2 MMS4 YBR098W NSAE2 MUS81 YDR386W NSAE2 POL32 YJR043C NSAE2 PUB1 YNL016W NSAE2 RAD27 YKL113C YSAE2 RAD50 YNL250W NSAE2 RNR1 YER070W N/DSAE2 RPL24A YGL031C NSAE2 RRM3 YHR031C YSAE2 RTT107 YHR154W NSAE2 SGS1 YMR190C YSAE2 SIS2 YKR072C NSAE2 SLX1 YBR228W NSAE2 SLX4 YLR135W NSAE2 SOD1 YJR104C NSAE2 SWE1 YJL187C NSAE2 TOP1 YOL006C NSAE2 WSS1 YHR134W NSAE2 YBR094W YBR094W NSGS1 ASF1 YJL115W YSGS1 CSM3 YMR048W YSGS1 ESC2 YDR363W YSGS1 HPR5 YJL092W YSGS1 MGS1 YNL218W YSGS1 MMS4 YBR098W YSGS1 MUS81 YDR386W YSGS1 POL32 YJR043C YSGS1 PUB1 YNL016W YSGS1 RAD27 YKL113C YSGS1 RAD50 YNL250W YSGS1 RNR1 YER070W YSGS1 RPL24A YGL031C YSGS1 RRM3 YHR031C YSGS1 RTT107 YHR154W YSGS1 SAE2 YGL175C YSGS1 SIS2 YKR072C YSGS1 SLX1 YBR228W YSGS1 SLX4 YLR135W YSGS1 SOD1 YJR104C YSGS1 SWE1 YJL187C YSGS1 TOP1 YOL006C YSGS1 WSS1 YHR134W YSGS1 YBR094W YBR094W YSIS2 ASF1 YJL115W NSIS2 CSM3 YMR048W NSIS2 ESC2 YDR363W NSIS2 HPR5 YJL092W NSIS2 MGS1 YNL218W N

Page 187: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

SIS2 MMS4 YBR098W NSIS2 MUS81 YDR386W NSIS2 POL32 YJR043C NSIS2 PUB1 YNL016W NSIS2 RAD27 YKL113C YSIS2 RAD50 YNL250W NSIS2 RNR1 YER070W N/DSIS2 RPL24A YGL031C NSIS2 RRM3 YHR031C NSIS2 RTT107 YHR154W NSIS2 SAE2 YGL175C NSIS2 SGS1 YMR190C YSIS2 SLX1 YBR228W NSIS2 SLX4 YLR135W NSIS2 SOD1 YJR104C YSIS2 SWE1 YJL187C NSIS2 TOP1 YOL006C NSIS2 WSS1 YHR134W NSIS2 YBR094W YBR094W NSLX1 ASF1 YJL115W NSLX1 CSM3 YMR048W NSLX1 ESC2 YDR363W YSLX1 HPR5 YJL092W NSLX1 MGS1 YNL218W NSLX1 MMS4 YBR098W NSLX1 MUS81 YDR386W NSLX1 POL32 YJR043C NSLX1 PUB1 YNL016W NSLX1 RAD27 YKL113C NSLX1 RAD50 YNL250W NSLX1 RNR1 YER070W N/DSLX1 RPL24A YGL031C NSLX1 RRM3 YHR031C NSLX1 RTT107 YHR154W NSLX1 SAE2 YGL175C NSLX1 SGS1 YMR190C YSLX1 SIS2 YKR072C NSLX1 SLX4 YLR135W NSLX1 SOD1 YJR104C NSLX1 SWE1 YJL187C NSLX1 TOP1 YOL006C NSLX1 WSS1 YHR134W NSLX1 YBR094W YBR094W NSLX4 ASF1 YJL115W NSLX4 CSM3 YMR048W NSLX4 ESC2 YDR363W YSLX4 HPR5 YJL092W NSLX4 MGS1 YNL218W NSLX4 MMS4 YBR098W NSLX4 MUS81 YDR386W NSLX4 POL32 YJR043C NSLX4 PUB1 YNL016W NSLX4 RAD27 YKL113C NSLX4 RAD50 YNL250W NSLX4 RNR1 YER070W N/DSLX4 RPL24A YGL031C NSLX4 RRM3 YHR031C NSLX4 RTT107 YHR154W NSLX4 SAE2 YGL175C NSLX4 SGS1 YMR190C YSLX4 SIS2 YKR072C NSLX4 SLX1 YBR228W NSLX4 SOD1 YJR104C NSLX4 SWE1 YJL187C NSLX4 TOP1 YOL006C NSLX4 WSS1 YHR134W N

Page 188: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

SLX4 YBR094W YBR094W NSOD1 ASF1 YJL115W YSOD1 CSM3 YMR048W NSOD1 ESC2 YDR363W NSOD1 HPR5 YJL092W NSOD1 MGS1 YNL218W NSOD1 MMS4 YBR098W NSOD1 MUS81 YDR386W NSOD1 POL32 YJR043C YSOD1 PUB1 YNL016W NSOD1 RAD27 YKL113C YSOD1 RAD50 YNL250W YSOD1 RNR1 YER070W N/DSOD1 RPL24A YGL031C NSOD1 RRM3 YHR031C NSOD1 RTT107 YHR154W YSOD1 SAE2 YGL175C NSOD1 SGS1 YMR190C YSOD1 SIS2 YKR072C NSOD1 SLX1 YBR228W NSOD1 SLX4 YLR135W NSOD1 SWE1 YJL187C NSOD1 TOP1 YOL006C NSOD1 WSS1 YHR134W NSOD1 YBR094W YBR094W NSWE1 ASF1 YJL115W N/DSWE1 CSM3 YMR048W N/DSWE1 ESC2 YDR363W N/DSWE1 HPR5 YJL092W N/DSWE1 MGS1 YNL218W N/DSWE1 MMS4 YBR098W N/DSWE1 MUS81 YDR386W N/DSWE1 POL32 YJR043C N/DSWE1 PUB1 YNL016W N/DSWE1 RAD27 YKL113C N/DSWE1 RAD50 YNL250W N/DSWE1 RNR1 YER070W N/DSWE1 RPL24A YGL031C N/DSWE1 RRM3 YHR031C N/DSWE1 RTT107 YHR154W N/DSWE1 SAE2 YGL175C N/DSWE1 SGS1 YMR190C N/DSWE1 SIS2 YKR072C N/DSWE1 SLX1 YBR228W N/DSWE1 SLX4 YLR135W N/DSWE1 SOD1 YJR104C N/DSWE1 TOP1 YOL006C N/DSWE1 WSS1 YHR134W N/DSWE1 YBR094W YBR094W N/DTOP1 ASF1 YJL115W NTOP1 CSM3 YMR048W NTOP1 ESC2 YDR363W NTOP1 HPR5 YJL092W NTOP1 MGS1 YNL218W NTOP1 MMS4 YBR098W NTOP1 MUS81 YDR386W NTOP1 POL32 YJR043C NTOP1 PUB1 YNL016W NTOP1 RAD27 YKL113C NTOP1 RAD50 YNL250W YTOP1 RNR1 YER070W N/DTOP1 RPL24A YGL031C NTOP1 RRM3 YHR031C NTOP1 RTT107 YHR154W NTOP1 SAE2 YGL175C NTOP1 SGS1 YMR190C Y

Page 189: Supplementary Online Material (S1llama.mshri.on.ca/courses/Biophysics205/Papers/zhu_2001... · 2009. 10. 19. · 4 The double-mutant query strain bni1∆::URA3 bim1∆::natR was constructed

TOP1 SIS2 YKR072C NTOP1 SLX1 YBR228W NTOP1 SLX4 YLR135W NTOP1 SOD1 YJR104C NTOP1 SWE1 YJL187C NTOP1 WSS1 YHR134W NTOP1 YBR094W YBR094W NWSS1 ASF1 YJL115W NWSS1 CSM3 YMR048W NWSS1 ESC2 YDR363W NWSS1 HPR5 YJL092W NWSS1 MGS1 YNL218W NWSS1 MMS4 YBR098W NWSS1 MUS81 YDR386W NWSS1 POL32 YJR043C NWSS1 PUB1 YNL016W NWSS1 RAD27 YKL113C NWSS1 RAD50 YNL250W NWSS1 RNR1 YER070W N/DWSS1 RPL24A YGL031C NWSS1 RRM3 YHR031C NWSS1 RTT107 YHR154W YWSS1 SAE2 YGL175C NWSS1 SGS1 YMR190C YWSS1 SIS2 YKR072C NWSS1 SLX1 YBR228W NWSS1 SLX4 YLR135W NWSS1 SOD1 YJR104C NWSS1 SWE1 YJL187C NWSS1 TOP1 YOL006C NWSS1 YBR094W YBR094W NYBR094W ASF1 YJL115W NYBR094W CSM3 YMR048W NYBR094W ESC2 YDR363W YYBR094W HPR5 YJL092W NYBR094W MGS1 YNL218W NYBR094W MMS4 YBR098W NYBR094W MUS81 YDR386W NYBR094W POL32 YJR043C NYBR094W PUB1 YNL016W NYBR094W RAD27 YKL113C NYBR094W RAD50 YNL250W NYBR094W RNR1 YER070W N/DYBR094W RPL24A YGL031C NYBR094W RRM3 YHR031C NYBR094W RTT107 YHR154W NYBR094W SAE2 YGL175C NYBR094W SGS1 YMR190C YYBR094W SIS2 YKR072C NYBR094W SLX1 YBR228W NYBR094W SLX4 YLR135W NYBR094W SOD1 YJR104C YYBR094W SWE1 YJL187C NYBR094W TOP1 YOL006C NYBR094W WSS1 YHR134W N