Prediction of Prediction of interactionsinteractions

Prediction of Prediction of interactionsinteractions

Gene fusionGene fusionGene fusionGene fusion

Gene neighboursGene neighbours

Gene co-ocurrenceGene co-ocurrence

human

drosophila

elegans

mouse

X X X X

X X X

X X X

X X X X

3

2

2

2 2

phylogeniesphylogenies

Proteína A

Proteína B

Profiles Profiles (phylogeny)(phylogeny)

Expand interactionsExpand interactions::Using “interologs”

DIP

COG members

Predicción basada en estructuraPredicción basada en estructuraPredicción basada en estructuraPredicción basada en estructura

Step 1: Building a grid for a molecule

Baldomero Oliva MiguelBaldomero Oliva Miguel

UUnniivveerrssiittaatt

PPoommppeeuu

FFaabbrraa

Surface and core regions

CORECOREVOLUMEVOLUME

Baldomero Oliva MiguelBaldomero Oliva Miguel

UUnniivveerrssiittaatt

PPoommppeeuu

FFaabbrraa

Baldomero Oliva MiguelBaldomero Oliva Miguel

UUnniivveerrssiittaatt

PPoommppeeuu

FFaabbrraa

Baldomero Oliva MiguelBaldomero Oliva Miguel

UUnniivveerrssiittaatt

PPoommppeeuu

FFaabbrraa

Convolution function:

core 4-

surface 1

outside 0

)(_

core 4

surface 1

outside 0

)(_

jstaticScore

imobileScore

Obtain the maximum C

),(_),(_),(1 1

yjistaticScorejximobileScoreyxCn

j

n

i

Baldomero Oliva MiguelBaldomero Oliva Miguel

UUnniivveerrssiittaatt

PPoommppeeuu

FFaabbrraa

Convolution function by Fourier Transform

))()((),(

)),(()()(

)_()(

)_()(

),(_),(_),(

1

1 1

yGxFyxC

yxCyGxF

staticScoreyG

mobileScorexF

yjistaticScorejximobileScoreyxCn

j

n

i

Baldomero Oliva MiguelBaldomero Oliva Miguel

UUnniivveerrssiittaatt

PPoommppeeuu

FFaabbrraa

Baldomero Oliva MiguelBaldomero Oliva Miguel

UUnniivveerrssiittaatt

PPoommppeeuu

FFaabbrraa

Baldomero Oliva MiguelBaldomero Oliva Miguel

UUnniivveerrssiittaatt

PPoommppeeuu

FFaabbrraa

Baldomero Oliva MiguelBaldomero Oliva Miguel

UUnniivveerrssiittaatt

PPoommppeeuu

FFaabbrraa

STRING STRING use of databaseuse of database

http://string.embl.dehttp://string.embl.de

Gene fusion

Gene neighborhood

Gene co-expression

Text Mining

Gene co-ocurrence

GRAPHGRAPH

GRAPHGRAPHDepth 2Depth 2

Prediction of Prediction of metabolic metabolic pathwayspathways

Prediction of Prediction of metabolic metabolic pathwayspathways

1.1.1.37 4.2.1.2

Oxalo-acetato Malato Fumarato

A-B

Pathway based in common substrates and products (except water)

Pathway based in common substrates and products (except water)

Applications Applications in in

proteomics proteomics

-

cDNA-Cy3 cDNA-Cy5

RNAextraction

ReversetranscriptionCy3-dCTP Cy5-dCTP

cDNA or oligo microarray

Referencesample

Testsample

mRNA

cDNA-Cy3 cDNA-Cy5

RNAextraction

ReversetranscriptionCy3- Cy5-

Referencesample

Testsample

Block Column Row ID F649 Median B649 Mean F550 Median B550 Mean ...1 1 1 gen 1 5356 240 11532 256 ...1 2 1 gen 1 5472 298 12293 221 ...1 3 1 gen 2 8986 279 12788 295 ...1 4 1 gen 2 6729 300 10520 364 ...1 5 1 gen 3 8981 318 18099 276 ...1 6 1 gen 3 9287 391 20459 308 ...1 7 1 gen 4 5138 358 11082 434 ...1 8 1 gen 4 5438 332 9594 257 ...1 9 1 gen 5 7634 356 13316 363 ...1 10 1 gen 5 9056 405 14402 291 ...1 11 1 gen 6 12181 701 16383 433 ...1 12 1 gen 6 15159 552 18793 263 ...1 13 1 gen 7 6805 243 14445 298 ...1 14 1 gen 7 6715 261 13874 199 ...1 15 1 gen 8 6073 319 12385 439 ...1 16 1 gen 8 5041 355 9371 335 ...

... ... ... ... ... ... ... ... ...

Dr. L. SumoyDr. L. Sumoy(CRG)(CRG)

metastasis metastasistumor tumorpH

68.8

6405

Mw4 7

28.4

21.7

16.8

9.1

4511

7505

2202

8401

5004

7202

8301

7201

7109

7004

7115

8201

8204

2303

5203

5201

Dra. A. Sierra (IRO)Dra. A. Sierra (IRO)

799.0 1339.4 1879.8 2420.2 2960.6 3501.0

Mass (m/z)

0

1206.4

0

10

20

30

40

50

60

70

80

90

100

% In

tens

ity

Spec #1=>BC=>NR(2.00)[BP = 1211.7, 1206]1211.6717

1906.0343

1194.6158 1929.9591

862.4662 1348.8247

1476.7584 1863.06352296.04781939.0241

1734.97912718.07682265.0709

1307.7049 1972.02821718.8513 2873.65272333.07871112.1055 1523.7867 1944.0422 2632.79781297.0594843.5174 1730.9145 2951.7657 3173.18392320.52671092.5729 2138.16601494.4012 2642.15281919.94801289.7267870.5190 3112.6114 3305.18392901.5867

Dr. D. Andreu (UPF)Dr. D. Andreu (UPF)

aSpot No.

Protein Identity Acc. No. pIMr

(kDa)Function

Differential expressionin breast cancer

2202 Multicatalytic endopeptidase complex zeta chain

P28066 4.7 26.58 Proteolysis Su et al., 2001 ; Perou et al., 1999 ; Ross et al ,2000

2303 Tyrosine3/tryptophan5 NP_006752 4.6 29.33 Transduction

4511 ATP synthase beta chain P06576 5.3 56.53 Synthesis of ATP Chen et al, 2001

5004 Beta-tubulin cofactor A O75347 5.3 12.90 Complex Assembly Perou et al., 1999

5201 Ran-BP1 (Ran binding protein 1)

P34022 5.2 23.74 GTPase activating ____________

5203 My 032 protein AF061735 6.6 15.82 ___________ ____________

6405 F-actin capping protein alpha-1 subunit

P52907 5.5 33.07 Complex Assembly Su et al., 2001 ; Ross et al., 2000

7004 Stathmin 1 P16949 5.8 17.29 Transcription Perou et al, 1999 ; Curmi et al, 2000 ; Brattsand G., 2000 ; Bieche et al, 1998

7109 Familial Als mutant G37r IAZV_A 5.9 16.12 Redox Chandel, 2000

7115 Non-metastatic cells 1 protein nm-23

P15531 5.8 17.31 Transcription Su et al., 2001 ; Nakopoulou et al 1999 ; Kapranos, 1996

7201 Thioredoxin peroxidase B 1QMV_A 5.4 21.91 Redox Su et al., 2001 ; Perou et al., 1999; Ross et al, 2000 ; Husbeck et al ,2001 ; Berggren 2001 et al. ;

Harvey et al , 2001

7202 Glutathione transferase P09211 5.4 23.57 Glut. transferase Perou et al., 1999 ; Ross et al, 2000Dialyna et al, 2001; Ghalia et al, 2000;

Huang et al, 2000

7505 Aminoacylase 1 Q03154 5.8 46.08 Hydrolysis Su et al., 2001 ; Perou et al., 1999 ; Ross et al, 2000

8201 Hypothetical protein MGC15429 NP_116139 5.9 22.45 ___________ _____________

8204 Peroxiredoxin3 P30048 7.1 28.05 Redox Su et al., 2001 ; Perou et al., 1999 ; Ross et al, 2000

8301 Carbonyl reductase 3 O75828 5.8 31.23 Redox _____________

8401 Enolase 1 P06733 7.1 47.78 Transcription Su et al., 2001 ; Perou et al., 1999 ; Ross et al , 2000

SPOTSSPOTSSPOTSSPOTS

Proteinas identificadas

Proteinas propuestas

Galectin

Cathepsin D

Tubulin 5

GlyoxalaseATP synthase

HSP27

Prdx 4

Laminin R

Predicción estructural

STRING databaseDIP database

Help to Help to solve 2D solve 2D page gelspage gels

Apply on Apply on the graphthe graphApply on Apply on the graphthe graph

Filtering by Filtering by weight & weight & isoelectric isoelectric pointpoint

Filtering by Filtering by weight & weight & isoelectric isoelectric pointpoint

LISTA DE CANDIDATOS

LISTA DE CANDIDATOS

LISTA DE CANDIDATOS

LISTA DE CANDIDATOS

Explaining Explaining biological biological processesprocesses

Functional Functional interestinterestFunctional Functional interestinterest

FUNCIONAL GROUP(GO cluster)

A

FUNCIONAL GROUP

(GO cluster)

B