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Prediction of interactions. Gene fusion Gene neighbours.

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Presentation on theme: "Prediction of interactions. Gene fusion Gene neighbours."— Presentation transcript:

1 Prediction of interactions

2 Gene fusion

3 Gene neighbours

4 Gene co-ocurrence human drosophila elegans mouse XXXX XXX XXX XXXX 3 2 2 2 2

5 phylogenies Proteína A Proteína B

6 Profiles (phylogeny)

7 Expand interactions: Using interologs DIP COG members

8 Predicción basada en estructura

9 Step 1: Building a grid for a molecule

10

11

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14 Baldomero Oliva Miguel UniversitatPompeuFabra Surface and core regions COREVOLUME

15 Baldomero Oliva Miguel UniversitatPompeuFabra

16 UniversitatPompeuFabra

17 UniversitatPompeuFabra Convolution function: Obtain the maximum C

18 Baldomero Oliva Miguel UniversitatPompeuFabra Convolution function by Fourier Transform

19 Baldomero Oliva Miguel UniversitatPompeuFabra

20 UniversitatPompeuFabra

21 UniversitatPompeuFabra

22 UniversitatPompeuFabra

23 STRING use of database http://string.embl.de

24 Gene fusion

25 Gene neighborhood

26 Gene co-expression

27 Text Mining

28 Gene co-ocurrence

29 GRAPH

30 GRAPH Depth 2

31 Prediction of metabolic pathways

32

33 1.1.1.37 4.2.1.2 Oxalo-acetatoMalatoFumarato A-B

34 Pathway based in common substrates and products (except water)

35 Applications in proteomics

36 - cDNA-Cy3 cDNA-Cy5 RNA extraction Reverse transcription Cy3-dCTP Cy5-dCTP cDNA or oligo microarray Reference sample Test sample mRNA cDNA-Cy3 cDNA-Cy5 RNA extraction Reverse transcription Cy3- Cy5- Reference sample Test sample Dr. L. Sumoy (CRG)

37 Dra. A. Sierra (IRO)

38 Dr. D. Andreu (UPF)

39

40 a Spot No. Protein Identity Acc. No.pI M r (kDa) Function Differential expression in breast cancer 2202Multicatalytic endopeptidase complex zeta chain P280664.726.58ProteolysisSu et al., 2001 ; Perou et al., 1999 ; Ross et al,2000 2303Tyrosine3/tryptophan5NP_0067524.629.33Transduction 4511ATP synthase beta chainP065765.356.53Synthesis of ATPChen et al, 2001 5004Beta-tubulin cofactor AO753475.312.90Complex AssemblyPerou et al., 1999 5201Ran-BP1 (Ran binding protein 1) P340225.223.74GTPase activating____________ 5203My 032 proteinAF0617356.615.82_______________________ 6405F-actin capping protein alpha-1 subunit P529075.533.07Complex AssemblySu et al., 2001 ; Ross et al., 2000 7004Stathmin 1P169495.817.29Transcription Perou et al, 1999 ; Curmi et al, 2000 ; Brattsand G., 2000 ; Bieche et al, 1998 7109Familial Als mutant G37rIAZV_A5.916.12RedoxChandel, 2000 7115Non-metastatic cells 1 protein nm-23 P155315.817.31TranscriptionSu et al., 2001 ; Nakopoulou et al 1999 ; Kapranos, 1996 7201Thioredoxin peroxidase B1QMV_A5.421.91RedoxSu et al., 2001 ; Perou et al., 1999; Ross et al, 2000 ; Husbeck et al,2001 ; Berggren 2001 et al. ; Harvey et al, 2001 7202Glutathione transferaseP092115.423.57Glut. transferasePerou et al., 1999 ; Ross et al, 2000 Dialyna et al, 2001; Ghalia et al, 2000; Huang et al, 2000 7505Aminoacylase 1Q031545.846.08HydrolysisSu et al., 2001 ; Perou et al., 1999 ; Ross et al, 2000 8201Hypothetical protein MGC15429NP_1161395.922.45________________________ 8204Peroxiredoxin3P300487.128.05RedoxSu et al., 2001 ; Perou et al., 1999 ; Ross et al, 2000 8301Carbonyl reductase 3O758285.831.23Redox_____________ 8401Enolase 1P067337.147.78TranscriptionSu et al., 2001 ; Perou et al., 1999 ; Ross et al, 2000 SPOTSSPOTS

41 Proteinas identificadas Proteinas propuestas Galectin Cathepsin D Tubulin 5 GlyoxalaseATP synthase HSP27 Prdx 4 Laminin R Predicción estructural STRING database DIP database

42 Help to solve 2D page gels

43 Apply on the graph

44 Filtering by weight & isoelectric point

45 LISTA DE CANDIDATOS

46 Explaining biological processes

47 Functional interest

48 FUNCIONAL GROUP (GO cluster) A FUNCIONAL GROUP (GO cluster) B


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