Prediction of interactions Gene fusion Gene neighbours Gene
Prediction of interactions
Gene fusion
Gene neighbours
Gene co-ocurrence X X X X human X X X 3 2 2 2 X drosophila X elegans mouse 2
phylogenies Proteína B Proteína A
Profiles (phylogeny)
Expand interactions: Using “interologs” DIP COG members
Predicción basada en estructura
Step 1: Building a grid for a molecule
U n i v e r s i t a t Surface and core regions P o m p e u F a b r a CORE VOLUME Baldomero Oliva Miguel
U n i v e r s i t a t P o m p e u F a b r a Baldomero Oliva Miguel
U n i v e r s i t a t P o m p e u F a b r a Baldomero Oliva Miguel
U n i v e r s i t a t Convolution function: P o m p e u F a b r a Obtain the maximum C Baldomero Oliva Miguel
U n i v e r s i t a t Convolution function by Fourier Transform P o m p e u F a b r a Baldomero Oliva Miguel
U n i v e r s i t a t P o m p e u F a b r a Baldomero Oliva Miguel
U n i v e r s i t a t P o m p e u F a b r a Baldomero Oliva Miguel
U n i v e r s i t a t P o m p e u F a b r a Baldomero Oliva Miguel
U n i v e r s i t a t P o m p e u F a b r a Baldomero Oliva Miguel
STRING use of database http: //string. embl. de
Gene fusion
Gene neighborhood
Gene co-expression
Text Mining
Gene co-ocurrence
GRAPH
GRAPH Depth 2
Prediction of metabolic pathways
4. 2. 1. 2 1. 1. 1. 37 Oxalo-acetato Malato A-B Fumarato
Pathway based in common substrates and products (except water)
Applications in proteomics
Reference sample RNA extraction Test sample m. RNA Reverse transcription Cy 3 -d. CTP Cy 3 - c. DNA-Cy 3 Cy 5 -d. CTP Cy 5 - c. DNA-Cy 5 - c. DNA or oligo microarray Dr. L. Sumoy (CRG)
metastasis p. H 4 tumor 7 tumor metastasis Mw 68. 8 7505 4511 8401 6405 8301 28. 4 2303 5201 8204 2202 21. 7 7202 5203 7201 7109 7115 7004 16. 8 9. 1 8201 5004 Dra. A. Sierra (IRO)
Dr. D. Andreu (UPF)
SPOTS a. Spot Protein Identity Acc. No. p. I Mr (k. Da) Function 2202 Multicatalytic endopeptidase complex zeta chain P 28066 4. 7 26. 58 Proteolysis 2303 Tyrosine 3/tryptophan 5 NP_006752 4. 6 29. 33 Transduction 4511 ATP synthase beta chain P 06576 5. 3 56. 53 Synthesis of ATP Chen et al, 2001 5004 Beta-tubulin cofactor A O 75347 5. 3 12. 90 Complex Assembly Perou et al. , 1999 5201 Ran-BP 1 (Ran binding protein 1) P 34022 5. 2 23. 74 GTPase activating ______ 5203 My 032 protein AF 061735 6. 6 15. 82 ____________ 6405 F-actin capping protein alpha-1 subunit P 52907 5. 5 33. 07 Complex Assembly Su et al. , 2001 ; Ross et al. , 2000 7004 Stathmin 1 P 16949 5. 8 17. 29 Transcription Perou et al, 1999 ; Curmi et al, 2000 ; Brattsand G. , 2000 ; Bieche et al, 1998 7109 Familial Als mutant G 37 r IAZV_A 5. 9 16. 12 Redox Chandel, 2000 7115 Non-metastatic cells 1 protein nm -23 P 15531 5. 8 17. 31 Transcription Su et al. , 2001 ; Nakopoulou et al 1999 ; Kapranos, 1996 7201 Thioredoxin peroxidase B 1 QMV_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 P 09211 5. 4 23. 57 Glut. transferase Perou et al. , 1999 ; Ross et al, 2000 Dialyna et al, 2001; Ghalia et al, 2000; Huang et al, 2000 7505 Aminoacylase 1 Q 03154 5. 8 46. 08 Hydrolysis Su et al. , 2001 ; Perou et al. , 1999 ; Ross et al, 2000 8201 Hypothetical protein MGC 15429 NP_116139 5. 9 22. 45 _____________ 8204 Peroxiredoxin 3 P 30048 7. 1 28. 05 Redox Su et al. , 2001 ; Perou et al. , 1999 ; Ross et al, 2000 8301 Carbonyl reductase 3 O 75828 5. 8 31. 23 Redox _______ 8401 Enolase 1 P 06733 7. 1 47. 78 Transcription Su et al. , 2001 ; Perou et al. , 1999 ; Ross et al , 2000 No. Differential expression in breast cancer Su et al. , 2001 ; Perou et al. , 1999 ; Ross et al , 2000
Galectin Tubulin 5 STRING database DIP database Predicción estructural HSP 27 Cathepsin D Prdx 4 ATP synthase Laminin R Glyoxalase Proteinas identificadas Proteinas propuestas
Help to solve 2 D page gels
Apply on the graph
Filtering by weight & isoelectric point
E D A LIST S O T A D I D CAN
Explaining biological processes
Functional interest
FUNCIONAL GROUP (GO cluster) A FUNCIONAL GROUP (GO cluster) B
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