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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

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

12

13

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

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 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 P ProteolysisSu et al., 2001 ; Perou et al., 1999 ; Ross et al, Tyrosine3/tryptophan5NP_ Transduction 4511ATP synthase beta chainP Synthesis of ATPChen et al, Beta-tubulin cofactor AO Complex AssemblyPerou et al., Ran-BP1 (Ran binding protein 1) P GTPase activating____________ 5203My 032 proteinAF _______________________ 6405F-actin capping protein alpha-1 subunit P Complex AssemblySu et al., 2001 ; Ross et al., Stathmin 1P Transcription Perou et al, 1999 ; Curmi et al, 2000 ; Brattsand G., 2000 ; Bieche et al, Familial Als mutant G37rIAZV_A RedoxChandel, Non-metastatic cells 1 protein nm-23 P TranscriptionSu et al., 2001 ; Nakopoulou et al 1999 ; Kapranos, Thioredoxin peroxidase B1QMV_A RedoxSu et al., 2001 ; Perou et al., 1999; Ross et al, 2000 ; Husbeck et al,2001 ; Berggren 2001 et al. ; Harvey et al, Glutathione transferaseP Glut. transferasePerou et al., 1999 ; Ross et al, 2000 Dialyna et al, 2001; Ghalia et al, 2000; Huang et al, Aminoacylase 1Q HydrolysisSu et al., 2001 ; Perou et al., 1999 ; Ross et al, Hypothetical protein MGC15429NP_ ________________________ 8204Peroxiredoxin3P RedoxSu et al., 2001 ; Perou et al., 1999 ; Ross et al, Carbonyl reductase 3O Redox_____________ 8401Enolase 1P TranscriptionSu 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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