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Suppl. Table S3. Sarcoma gene expression signature shared by mouse Kras; p16p19null sarcomas and human RMS.
Probe Set ID Gene Symbol Gene title
Previously published association with
malignanciesReferences
207173_x_atCDH11
cadherin 11, type 2, OB-cadherin
(osteoblast)
CDH11 expression predicts survival in
patients with osteosarcoma.
Nakajima et al., 2007(1)
207172_s_at
209891_at SPC25
SPC25, NDC80 kinetochore
complex component, homolog (S. cerevisiae)
214452_at BCAT1branched chain
aminotransferase 1, cytosolic
Assciated with metastatic
medulloblastoma and chemotherapy-resistant
ovarian cancer.
De Bont et al., 2008; Ju et al., 2009
(2, 3)
206432_at HAS2 hyaluronan synthase 2
Expression of Has2 in highly invasive breast
cancer cell lines; HAS2 transfection of
fibrosarcoma cell line HT-1080 results in
enhanced tumorigenicity and anchorage-
independent growth.
Udabage etal., 2005; Kosaki et al., 1999
(4, 5)
218542_at CEP55 centromere protein E, 312kDa
Association with head and neck squamous cell carcinoma progression
Waseem et al., 2010(6)
212158_at SDC2 syndecan 2
Prognostic factor in esophagus carcinoma;
Increased expression in colon carcinoma cell
lines.
Huang et al., 2009; Han et al., 2004
(7, 8)
209647_s_at SOCS5 suppressor of High SOCS5 levels in Evans et al., 2007
cytokine signaling 5 breast cancer cell lines. (9)
202935_s_atSOX9
SRY (sex determining
region Y)-box 9
Associated with human soft-tissue
maliganncies
Soederstroem et al., 2002; Cajaiba et al.,
2010(10, 11)202936_s_at
211121_s_at DOK1
docking protein 1, 62kDa
(downstream of tyrosine kinase 1)
Functions as a tumor suppresor in the
hematopoietic system
Niki et al., 2004(12)
204463_s_at
EDNRA endothelin receptor type A204464_s_at
216235_s_at
203313_s_at TGIF1TGFB-induced
factor homeobox 1
201897_s_at CKS1BCDC28 protein
kinase regulatory subunit 1B
Associated with adverse outcomes in human
hepatocellular carcinoma, cutaneous
squamous cell carcinoma, multiple
myeloma.
Huang et al., 2010; Salgado et al., 2010; Chang et al., 2010
(13-15)
213506_at F2RL1coagulation factor
II (thrombin) receptor-like 1
210933_s_at
FSCN1
fascin homolog 1, actin-bundling
protein (Strongylocentrot
us purpuratus)
Correlates with progression/ adverse
outcomes in human non small cell lung cancer,
nasopharyngeal/ hepatocellular/
urothelial carcinoma.
Zhao et al., 2010; Wu et al., 2010; Iguchi et
al., 2009; Tong et al.,2005(16-20)201564_s_at
218009_s_at PRC1 protein regulator of cytokinesis 1
Upregulated in leiomyosarcoma
Skubitz and Skubitz, 2003 (21)
201666_at TIMP1TIMP
metallopeptidase inhibitor 1
Low serum levels in patients with high-
grade soft-tissue sarcomas; Induction of
TIMP1 in a fibrosarcona cell line (HT1080) suppresses
invasive potential.
Benassi et al., 2003; Tanaka et al., 1995
(22, 23)
203625_x_at SKP2S-phase kinase-
associated protein 2 (p45)
Target gene in PAX3-FKHR positive
rhabdomyosarcoma
Nishijo et al., 2009(24)
204026_s_at ZWINT ZW10 interactor
210495_x_at
FN1 Fibronectin
Increased Fibronectin-dependent
proliferation, adhesion and invasion of human fibrosarcoma cell line HT1080; Correlates
with disease progression in human renal cell carcinoma.
Waalkes et al., 2010(25)
211719_x_at
212464_s_at
214701_s_at
214702_at
216442_x_at
209832_s_at CDT1
chromatin licensing and
DNA replication factor 1
Highly expressed in human neoplastic
lesions of the colon
Bravou et al., 2005(26)
203418_at
CCNA2 cyclin A2 Associated with chemotherapy-resistant
ovarian cancer.
Ju et al., 2009(3)
213226_at
208712_atCCND1 cyclin D1
208711_s_at
204244_s_at DBF4 DBF4 homolog (S. cerevisiae)
CDC7-DBF4 overexpression in
various human malignancies.
Bonte et al., 2008(27)
204033_at TRIP13thyroid hormone
receptor interactor 13
Genomic copy number changes in early stages of non small cell lung
cancer.
Kang et al., 2008(28)
213139_at SNAI2 snail homolog 2 (Drosophila)
Mediates invasiveness in human gliomas and
prostate cancer cell lines.
Emadi et al., 2010; Yang et al., 2010
(29, 30)
207466_at GAL galanin prepropeptide
Putative biomarker in human squamous cell
carcinoma
Sugimoto et al., 2009.(31)
205249_at EGR2 early growth response 2
Induces apoptosis in various cancer cell lines
Unoki and Nakamura, 2003 (32)
201631_s_at IER3 immediate early response 3
Association with pancreatic
adenocarcinoma; stress-inducible protein
regulating cell proliferation/ apoptosis.
Sasada et al., 2008(33)
203111_s_at PTK2BPTK2B protein
tyrosine kinase 2 beta
Stimulates glioma cell migration
Lipinski et al., 2005(34)
206115_at EGR3 early growth response 3
Predictive of adverse outcome in human
breast cancer
Suzuki et al., 2007(35)
208621_s_at EZR ezrin Upregulated in osteosarcoma
compared to benign bone tumors; Linked
to the metastatic behavior of
rhabdomyosarcoma.
Wan et al., 2009; Yu et al., 2004
(23, 36)
211564_s_at
PDLIM4 PDZ and LIM domain 4
Reduces prostate cancer cell growth
Vanaja et al., 2009(37)218691_s_at
214175_x_at
217997_atPHLDA1
pleckstrin homology-like
domain, family A, member 1
Downregulation in prognostically poor breast cancer and
metastatic melanoma.
Nagai et al., 2007; Neef et al., 2002
(38, 39)217999_s_at
201286_at
SDC1 syndecan 1
Expression in epitheloid sarcoma, synovial sarcoma, GIST, malignant
schwannoma; Transfection of
fibrosarcoma cell line HT-1080 results in
increased growth rate and more lung
metastases.
Orosz and Kopper, 2001; Peterfia et al.,
2006(40, 41)201287_s_at
213100_at UNC5B Unc-5 homolog B (C. elegans)
221269_s_at SH3BGRL3
SH3 domain binding glutamic acid-rich protein
like 3
205047_s_at ASNS asparagine synthetase
New biomarker in ovarian cancer.
Lorenzi and Weinstein, 2009 (42)
219148_at PBK PDZ binding kinase EWS/ FLI1 target Herrero-Martin et al.,
2009 (43)
201930_at MCM6 minichromosome maintenance
complex component 6
MCM6 identifies progressive
chondrosarcoma
Helfenstein et al., 2004(44)
208808_s_at HMGB2 high-mobility group box 2
Expression correlates with progression of
squamous cell carcinoma of the skin.
Sharma et al., 2008(45)
212836_at POLD3
polymerase (DNA-directed), delta 3, accessory
subunit
205628_at PRIM2primase, DNA, polypeptide 2
(58kDa)
205180_s_at ADAM8ADAM
metallopeptidase domain 8
ADAM8 expression crrelates with
invasiveness in human pancreatic cancer, prostate cancer and
brain tumors.
Mochizuki and Okada, 2007; Valkovskaya et al., 2007; Fritzsche et
al., 2006; Wildeboer et al., 2006 (46-49)
202052_s_at RAI14 retinoic acid induced 14
209505_atNR2F1
Nuclear receptor subfamily 2,
group F, member 1209506_s_at
219117_s_atFKBP11
FK506 binding protein 11, 19
kDa219118_at
208258_s_at GAS2L1growth arrest-
specific 2 like 1Diminuished expression levels in acute myeloid
leukemia
Desmond et al., 2007(50)
200698_at KDELR2 KDEL(Lys-Asp-Glu-Leu)
endoplasmic reticulum protein retention receptor
2
200699_at
200700_s_at
201862_s_atLRRFIP1
leucine rich repeat (in FLII)
interacting protein 1211452_x_at
212364_at MYO1B myosin IB
208452_x_atMYO9B myosin IXB
217297_s_at
216804_s_at PDLIM5 PDZ and LIM domain 5
206636_at RASA2 RAS p21 protein activator 2
209146_at SC4MOL sterol-C4-methyl oxidase-like
201920_at SLC20A1
solute carrier family 20
(phosphate transporter), member 1
202088_at SLC39A6
solute carrier family 39 (zinc
transporter), member 6
Breast-cancer associated protein
Taylor et al., 2003(51)
213164_at SLC5A3
solute carrier family 5 (sodium/
myoinositol cotransporter),
member 3
209218_at SQLE squalene epoxidase
Potential biomarker in human prostate cancer,
Zhao et al., 2010; Harada et al., 2009;
pancreatic adenocarcinoma, breast
cancer.
Helms et al., 2008(52-54)
213562_s_at
213577_at
203476_at TPBG trophoblast glycoprotein
Upregulated in gastrointestinal stromal tumors
Gromova et al., 2009(55)
209191_at TUBB6 tubulin, beta 6
201397_at PHGDH phosphoglycerate dehydrogenase
High expression associated with adverse
outcome in breast cancer
Pollari et al., 2010(56)
219161_s_atCKLF chemokine-like
factor221058_s_at
206704_at CLCN5 chloride channel 5
207030_s_atCSRP2
cysteine and glycine-rich
protein 2
Expressed in hepatocellular
carcinoma.
Midorikawa et al., 2002(57)
211126_s_at
214074_s_at CTTN cortactin
Cortactin staining in rhabdomyosarcomas, leiomyosarcomas, one infantile fibrosarcoma
and one MFH.
Parham et al., 1995(58)
201095_at DAP death-associated protein
203279_at EDEM1
ER degradation enhancer,
mannosidase alpha-like 1
206501_x_at ETV1 ets variant 1 Rare EWS fusions in Ewings family tumors Wang et al., 2007
include two EWS/ETV1 fusions. (59)
217053_x_at
217061_s_at
221910_at
221911_at
207178_s_at FRK fyn-related kinase
Associates with Rb; Functions as a tumor
suppressor in mammary epithelial cells by
regulating PTEN protein stability and function.
Craven et al., 1995; Yim et al., 2009
(60, 61)
204472_at GEM
GTP binding protein
overexpressed in skeletal muscle
208460_at GJC1gap junction
protein, gamma 1, 45kDa
214472_at HIST1H2AD histone cluster 1, H2ad
200644_at MARCKSL1 MARCKS-like 1 Expression in prostate cancer
Romanuik et al., 2009(62)
203228_at PAFAH1B3
platelet-activating factor
acetylhydrolase, isoform Ib,
subunit 3 (29kDa)
207505_at PRKG2protein kinase,
cGMP-dependent, type II
203423_at RBP1 retinol binding protein 1, cellular
204336_s_at RGS19 regulator of G-protein signaling
19
219493_at SHCBP1 SHC SH2-domain binding protein 1
37831_at SIPA1L3signal-induced proliferation-
associated 1 like 3
212944_at SLC5A3
solute carrier family 25
(mitochondrial carrier; phosphate carrier), member
24
204619_s_at
VCAN versican
Contributes to cancer invasion and
mestastasis; expressed in human epithelial
cancers.
Ricciardelli et al., 2009(63)
204620_s_at
215646_s_at
221731_x_at
209765_at ADAM19
ADAM metallopeptidase
domain 19 (meltrin beta)
Upregulated in brain tumors
Wildeboer et al., 2006(49)
219693_at AGPAT4
1-acylglycerol-3-phosphate O-
acyltransferase 4 (lysophosphatidic
acid acyltransferase,
delta)
202207_atARL4C ADP-ribosylation
factor-like 4C
202208_s_at
203404_at ARMCX2armadillo repeat containing, X-
linked 2
200920_s_at BTG1
B-cell translocation gene
1, anti-proliferative
Bcl-2-regulated mediator of apoptosis in
breast cancer cells
Nahta et al., 2006(64)
201850_at CAPGcapping protein (actin filament),
gelsolin-like
Linked to motility of pancreatic cancer cells;
Expressed in serous ovarian
adenocarcinomas.
Thompson et al., 2007; Partheen et al., 2008
(65, 66)
218802_at CCDC109Bcoiled-coil
domain containing 1
210821_x_at CENPA centromere protein A
CENPA overexpression promotes genome instability in pRb-
depleted human cells.
Amato et al, 2009(16)
203044_at CHSY1 chondroitin sulfate synthase 1
217025_s_at DBN1 drebrin 1
202719_s_at TEStestis derived
transcript (3 LIM domains)
Putative tumor suppressor in human
epithelial, hematopoietic malignancies and
human glioblastoma.
Gunduz et al., 2009; Mueller et al., 2007; Drusco et al., 2005; Chene et al., 2004
(67-70)
213253_at SMC2structural
maintenance of chromosomes 2
204222_s_at GLIPR1 GLI pathogenesis-related 1
209372_x_at TUBB2A tubulin, beta 2A
205122_at TMEFF1 transmembrane protein with EGF-
like and two follistatin-like
Gery et al., 2003(71)
domains 1
As
201952_atALCAM
activated leukocyte cell
adhesion molecule
Association with breast cancer; Expression in
pancreatic adenocarcinoma
predicts worse outcome.
Davies et al., 2008; Kahlert et al., 2009
(72, 73)201951_at
204962_s_at CENPA centromere protein A
CENPA overexpression promotes genome instability in pRb-
depleted human cells.
Amato et al, 2009(16)
204170_s_at CKS2
CDC28 protein kinase
regulatory subunit 2
Upregulated in leiomyosarcomas
Skubitz and Skubitz, 2003 (21)
204558_at RAD54L RAD54-like (S. cerevisiae)
205046_at CENPE centromere protein E, 312kDa
Expressed in neuroblastoma, regulates cell proliferation;
Upregulated in chemoresistant ovarian
cancer.
Balamuth et al., 2010; Ju et al., 2009
(3, 74)
202870_s_at CDC20cell division cycle
20 homolog (S. cerevisiae)
High levels of CDC20 associated with poor outcomes in ovarian
cancer
Ouellet et al., 2006(75)
207143_at CDK6 cyclin-dependent kinase 6
Inhibition of cyclin-dependent kinase 4/6
activity arrests proliferation in
myoblasts/ rhabdomyosarcoma-
derived cells.
Saab et al., 2006(76)
220085_at HELLS helicase, lymphoid-specific
Potential serum marker for melanoma
metastasis; Association with head and neck
squamous cell carcinoma.
Kim et al., 2010; Waseem et al., 2010
(6, 77)
203344_s_at RBBP8 retinoblastoma binding protein 8
201291_s_atTOP2A
topoisomerase (DNA) II alpha
170kDa
Upregulated in leiomyosarcomas
Skubitz and Skubitz, 2003 (21)
201292_at
212345_s_at CREB3L2AMP responsive element binding protein 3-like 2
FUS-CREB3L1/L2 fusion in low-grade
myoxoid fibrosarcoma
Matsuyama et al., 2006 (78)
203028_s_at CYBAcytochrome b-
245, alpha polypeptide
204137_at GPR137B G protein-coupled receptor 137B
220063_at GSTCD
glutathione S-transferase, C-
terminal domain containing
200618_at LASP1 LIM and SH3 protein 1
Upregulated in human breast cancer, ovarian cancer, bladder cancer,
medulloblastoma; Linked to cell
proliferation, migration and metastasis.
Traenka et al., 2010; Chiyomaru et al., 2010; Grunewald et al., 2007;
Asaka et al., 2006(79-82)
221011_s_at LBHlimb bud and heart development homolog (mouse)
212843_at NCAM1neural cell adhesion
molecule 1
Nearly ubiquitous NCAM in alveolar
rhabdomyosarcoma; NCAM expression in synovial sarcomas;
Bahrami et al, 2008; Hartel et al, 2007;
Molenaar and Muntinghe, 1998
NCAM widely expressed in
(83-85)
217963_s_at NGFRAP1
nerve growth factor receptor (TNFRSF16)
associated protein 1
215743_at NMT2N-
myristoyltransferase 2
Potential chemoresistance gene
in osteosarcoma; Expression in human
brain tumors and human colon cancer.
Walters et al., 2008; Lu et al., 2005;
Selvakumar et al., 2006 (86-88)
204866_at PHF16 PHD finger protein 16
204944_at PTPRGprotein tyrosine
phosphatase, receptor type, G
Candidate tumor suppressor gene in
nasopharyngeal carcinoma
Cheung et al., 2008(89)
217775_s_atRDH11
retinol dehydrogenase 11 (all-trans/ 9-cis/
11-cis)217776_at
204342_at SLC25A24
solute carrier family 25
(mitochondrial carrier; phosphate carrier), member
24
204913_s_at SOX11SRY (sex
determining region Y)-box 11
Expressed in human malignant gliomas, medulloblastoma,
hematopoietic malignancies, ovarian
Weigle et al., 2005; De Bont et al., 2008;
Gustavsson et al., 2010; Brennan et al., 2009
cancer. Regulates cell growth.
(2, 90-92)
209118_s_at TUBA1A tubulin, alpha 1a
202391_at BASP1
brain abundant, membrane
attached signal protein 1
Reduced expression in hepatocellular
carcinoma
Moribe et al., 2008(93)
217985_s_at BAZ1Abromodomain
adjacent to zinc finger domain, 1A
208838_atCAND1
cullin-associated and neddylation-
dissociated 1207483_s_at
202806_at DBN1 drebrin 1
202539_s_atHMGCR
3-hydroxy-3-methylglutaryl-Coenzyme A
reductase202540_s_at
204886_atPLK4 polo-like kinase 4
(Drosophila)
Plk4 haploinsufficiency causes mitotic infidelity
and carcinogenesis
Ko et al., 2005(94)
204887_s_at
211181_x_at RUNX1runt-related transcription
factor 1
Most frequent target of chromosomal
rearrangements in human leukemia.
Lichtinger et al., 2010(95)
201645_at TNC tenascin C
Promotes survival of human
chondrosarcoma cells in vitro
Jang and Chung, 2005(96)
204995_at CDK5R1 cyclin-dependent kinase 5,
regulatory subunit 1 (p35)
210367_s_at PTGES prostaglandin E synthase
215813_s_at PTGS1
prostaglandin-endoperoxide
synthase 1 (prostaglandin G/H synthase
and cyclooxygenase)
Expressed in Kaposi's sarcomas
Rossiello et al., 2007(97)
200745_s_atGNB1
guanine nucleotide
binding protein (G protein), beta polypeptide 1
Decreased expression in unfavorable NB tumors
Thorell et al., 2009(98)
200746_s_at
218468_s_at GREM1
gremlin 1, cysteine knot superfamily,
homolog (Xenopus laevis)
Overexpression in human epithelial
tumors and sarcomas.
Namkoong et al., 2006(99)
202954_at UBE2Cubiquitin-
conjugating enzyme E2C
Upregulated in leiomyosarcomas
Skubitz and Skubitz, 2003 (21)
201250_s_at SLC2A1
solute carrier family 2
(facilitated glucose
transporter), member 1
Expression in human rhabdomyosarcoma
cell line RD; Expressed in 50% of
leiomyosarcomas, but not in leiomyomas.
Ito et al., 2000; Rao et al., 1999 (100, 101)
218399_s_at CDCA4 cell division cycle associated 4
201875_s_atMPZL1 myelin protein
zero-like 1210594_x_at
220892_s_at PSAT1 phosphoserine aminotransferase
Expressed in human colon tumors; PSAT1
Vie et al., 2008(102)
1
overexpression increases growth rate/
survival of colon carcinoma cell line.
204141_at TUBB2A tubulin, beta 2A
203440_at CDH2cadherin 2, type
1, N-cadherin (neuronal)
Expressed in human rhabdomyosarcoma; Expressed in human pleural mesothelioma
and melanoma.
Soler et al., 1993; Han et al., 1999; Attis et
al., 2006(103-105)
209081_s_at COL18A1 collagen, type XVIII, alpha 1
Expressed in osteosarcoma Kim et al., 2009 (106)
221059_s_at COTL1 coactosin-like 1 (Dictyostelium)
217992_s_at EFHD2EF-hand domain family, member
D2
206335_at GALNSgalactosamine (N-acetyl)-6-sulfate
sulfatase
209651_at TGFB1I1
transforming growth factor beta
1 induced transcript 1
205123_s_at TMEFF1
transmembrane protein with EGF-
like and two follistatin-like
domains 1
Putative tumor suppressor gene in
human brain cancers
Gery et al., 2003(71)
214085_x_at GLIPR1 GLI pathogenesis-related 1
204240_s_at SMC2structural
maintenance of chromosomes 2
202720_at TES testis derived transcript (3 LIM
Putative tumor suppressor in human
Gunduz et al., 2009; Mueller et al., 2007;
domains)epithelial, hematopoietic
malignancies and human glioblastoma.
Drusco et al., 2005; Chene et al., 2004
(67-70)
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