Modular decomposition of protein-protein interaction networks

Genome Biology

Volumn 5, Issue 8, 2004, Pages

  Gagneur, Julien ^a,b   Krause, Roland ^a   Bouwmeester, Tewis ^a   Casari, Georg ^a  

^a GLAXOSMITHKLINE   (United Kingdom)

^b Ecole Centrale de Paris   (France)

Author keywords

Additional Data File; Logical Organization; Maximal Clique; Parallel Module; Series Module

Indexed keywords

DNA DIRECTED RNA POLYMERASE; IMMUNOGLOBULIN ENHANCER BINDING PROTEIN; MULTIPROTEIN COMPLEX; SACCHAROMYCES CEREVISIAE PROTEIN; TRANSCRIPTION FACTOR; TUMOR NECROSIS FACTOR ALPHA;

ALGORITHM; ARTICLE; BIOLOGY; CHEMISTRY; DRUG EFFECT; GENE EXPRESSION REGULATION; GENETICS; METABOLISM; PROTEIN BINDING; SACCHAROMYCES CEREVISIAE; SIGNAL TRANSDUCTION;

ALGORITHMS; COMPUTATIONAL BIOLOGY; DNA-DIRECTED RNA POLYMERASES; GENE EXPRESSION REGULATION, FUNGAL; MULTIPROTEIN COMPLEXES; NF-KAPPA B; PROTEIN BINDING; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; SIGNAL TRANSDUCTION; TRANSCRIPTION FACTORS; TUMOR NECROSIS FACTOR-ALPHA;

EID: 13844304634     PISSN: 14747596     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/gb-2004-5-8-r57     Document Type: Article

References (38)

1. Ito T, Chiba T, Ozawa R, Yoshida M, Hattori M, Sakaki Y: A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc Natl Acad Sci USA. 2001, 98: 4569-4574. 10.1073/pnas.061034498. DOI: 10.1073/pnas.061034498
2. Uetz P, Giot L, Cagney G, Mansfield TA, Judson RS, Knight JR, Lockshon D, Narayan V, Srinivasan M, Pochart P, et al: A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature. 2000, 403: 623-627. 10.1038/35001009. DOI: 10.1038/35001009
3. Ho Y, Gruhler A, Heilbut A, Bader GD, Moore L, Adams SL, Millar A, Taylor P, Bennett K, Boutilier K, et al: Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature. 2002, 415: 180-183. 10.1038/415180a. DOI: 10.1038/415180a
4. Gavin AC, Bosche M, Krause R, Grandi P, Marzioch M, Bauer A, Schultz J, Rick JM, Michon AM, Cruciat CM, et al: Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature. 2002, 415: 141-147. 10.1038/415141a. DOI: 10.1038/415141a
5. Deng M, Sun F, Chen T: Assessment of the reliability of protein-protein interactions and protein function prediction. Pac Symp Biocomput. 2003, 140-151.
6. Bader GD, Hogue CW: An automated method for finding molecular complexes in large protein interaction networks. BMC Bioinformatics. 2003, 4: 2-10.1186/1471-2105-4-2. DOI: 10.1186/1471-2105-4-2
7. Spirin V, Mirny LA: Protein complexes and functional modules in molecular networks. Proc Natl Acad Sci USA. 2003, 100: 12123-12128. 10.1073/pnas.2032324100. DOI: 10.1073/pnas.2032324100
8. Möhring RH: Algorithmic aspects of the substitution decomposition in optimization over relations, set systems and boolean functions. Annls Operations Res. 1985, 4: 195-225. DOI: 10.1007/BF02022041
9. Möhring RH, Radermacher FJ: Substitution decomposition for discrete structures and connections with combinatorial optimization. Annls Disc Math. 1984, 19: 257-356.
10. Rigaut G, Shevchenko A, Rutz B, Wilm M, Mann M, Seraphin B: A generic protein purification method for protein complex characterization and proteome exploration. Nat Biotechnol. 1999, 17: 1030-1032. 10.1038/13732. DOI: 10.1038/13732
11. Fields S, Song O: A novel genetic system to detect protein-protein interactions. Nature. 1989, 340: 245-246. 10.1038/340245a0. DOI: 10.1038/340245a0
12. Yang H, Jiang W, Gentry M, Hallberg RL: Loss of a protein phosphatase 2A regulatory subunit (Cdc55p) elicits improper regulation of Swe1p degradation. Mol Cell Biol. 2000, 20: 8143-8156. 10.1128/MCB.20.21.8143-8156.2000. DOI: 10.1128/MCB.20.21.8143-8156.2000
13. Cramer P, Bushnell DA, Fu J, Gnatt AL, Maier-Davis B, Thompson NE, Burgess RR, Edwards AM, David PR, Kornberg RD: Architecture of RNA polymerase II and implications for the transcription mechanism. Science. 2000, 288: 640-649. 10.1126/science.288.5466.640. DOI: 10.1126/science.288.5466.640
14. Rubbi L, Labarre-Mariotte S, Chedin S, Thuriaux P: Functional characterization of ABC10alpha, an essential polypeptide shared by all three forms of eukaryotic DNA-dependent RNA polymerases. J Biol Chem. 1999, 274: 31485-31492. 10.1074/jbc.274.44.31485. DOI: 10.1074/jbc.274.44.31485
15. Lalo D, Carles C, Sentenac A, Thuriaux P: Interactions between three common subunits of yeast RNA polymerases I and III. Proc Natl Acad Sci USA. 1993, 90: 5524-5528. DOI: 10.1073/pnas.90.12.5524
16. Henry NL, Campbell AM, Feaver WJ, Poon D, Weil PA, Kornberg RD: TFIIF-TAF-RNA polymerase II connection. Genes Dev. 1994, 8: 2868-2878. DOI: 10.1101/gad.8.23.2868
17. Kim YJ, Bjorklund S, Li Y, Sayre MH, Kornberg RD: A multiprotein mediator of transcriptional activation and its interaction with the C-terminal repeat domain of RNA polymerase II. Cell. 1994, 77: 599-608. 10.1016/0092-8674(94)90221-6. DOI: 10.1016/0092-8674(94)90221-6
18. Cairns BR, Lorch Y, Li Y, Zhang M, Lacomis L, Erdjument-Bromage H, Tempst P, Du J, Laurent B, Kornberg RD: RSC, an essential, abundant chromatin-remodeling complex. Cell. 1996, 87: 1249-1260. 10.1016/S0092-8674(00)81820-6. DOI: 10.1016/S0092-8674(00)81820-6
19. Cairns BR, Kim YJ, Sayre MH, Laurent BC, Kornberg RD: A multisubunit complex containing the SWI1/ADR6, SWI2/SNF2, SWI3, SNF5, and SNF6 gene products isolated from yeast. Proc Natl Acad Sci USA. 1994, 91: 1950-1954. DOI: 10.1073/pnas.91.5.1950
20. Szerlong H, Saha A, Cairns BR: The nuclear actin-related proteins Arp7 and Arp9: a dimeric module that cooperates with architectural proteins for chromatin remodeling. EMBO J. 2003, 22: 3175-3187. 10.1093/emboj/cdg296. DOI: 10.1093/emboj/cdg296
21. Bouwmeester T, Bauch A, Ruffner H, Angrand PO, Bergamini G, Croughton K, Cruciat C, Eberhard D, Gagneur J, Ghidelli S, et al: A physical and functional map of the human TNF-alpha/NF-kappaB signal transduction pathway. Nat Cell Biol. 2004, 6: 97-105. 10.1038/ncb1086. DOI: 10.1038/ncb1086
22. A physical map of the human TNF-NFkappaB signal transduction pathway. [http://tnf.cellzome.com]
23. Bader GD, Hogue CW: Analyzing yeast protein-protein interaction data obtained from different sources. Nat Biotechnol. 2002, 20: 991-997. 10.1038/nbt1002-991. DOI: 10.1038/nbt1002-991
24. Van Huffel S, Delaei F, Heyninck K, De Valck D, Beyaert R: Identification of a novel A20-binding inhibitor of nuclear factor-kappa B activation termed ABIN-2. J Biol Chem. 2001, 276: 30216-30223. 10.1074/jbc.M100048200. DOI: 10.1074/jbc.M100048200
25. Belich MP, Salmeron A, Johnston LH, Ley SC: TPL-2 kinase regulates the proteolysis of the NF-kappaB-inhibitory protein NF-kappaB1 p105. Nature. 1999, 397: 363-368. 10.1038/16946. DOI: 10.1038/16946
26. Holme P, Huss M, Jeong H: Subnetwork hierarchies of biochemical pathways. Bioinformatics. 2003, 19: 532-538. 10.1093/bioinformatics/btg033. DOI: 10.1093/bioinformatics/btg033
27. Ravasz E, Somera AL, Mongru DA, Oltvai ZN, Barabasi AL: Hierarchical organization of modularity in metabolic networks. Science. 2002, 297: 1551-1555. 10.1126/science.1073374. DOI: 10.1126/science.1073374
28. Gagneur J, Jackson DB, Casari G: Hierarchical analysis of dependency in metabolic networks. Bioinformatics. 2003, 19: 1027-1034. 10.1093/bioinformatics/btg115. DOI: 10.1093/bioinformatics/btg115
29. Snel B, Bork P, Huynen MA: The identification of functional modules from the genomic association of genes. Proc Natl Acad Sci USA. 2002, 99: 5890-5895. 10.1073/pnas.092632599. DOI: 10.1073/pnas.092632599
30. Ju BH, Han K: Complexity management in visualizing protein interaction networks. Bioinformatics. 2003, 19 (Suppl 1): I177-I179. 10.1093/bioinformatics/btg1022. DOI: 10.1093/bioinformatics/btg1022
31. Schuster S, Pfeiffer T, Moldenhauer F, Koch I, Dandekar T: Exploring the pathway structure of metabolism: decomposition into subnetworks and application to Mycoplasma pneumoniae. Bioinformatics. 2002, 18: 351-361. 10.1093/bioinformatics/18.2.351. DOI: 10.1093/bioinformatics/18.2.351
32. Hartwell LH, Hopfield JJ, Leibler S, Murray AW: From molecular to modular cell biology. Nature. 1999, 402: C47-C52. 10.1038/35011540. DOI: 10.1038/35011540
33. Alon U: Biological networks: the tinkerer as an engineer. Science. 2003, 301: 1866-1867. 10.1126/science.1089072. DOI: 10.1126/science.1089072
34. Milo R, Shen-Orr S, Itzkovitz S, Kashtan N, Chklovskii D, Alon U: Network motifs: simple building blocks of complex networks. Science. 2002, 298: 824-827. 10.1126/science.298.5594.824. DOI: 10.1126/science.298.5594.824
35. Remy E, Mosse B, Chaouiya C, Thieffry D: A description of dynamical graphs associated to elementary regulatory circuits. Bioinformatics. 2003, 19 (Suppl 2): II172-II178.
36. Segal E, Shapira M, Regev A, Pe'er D, Botstein D, Koller D, Friedman N: Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data. Nat Genet. 2003, 34: 166-176. 10.1038/ng1165. DOI: 10.1038/ng1165
37. McConnell RM, Spinrad JP: Ordered vertex partitioning. Disc Math Theor Comp Sci. 2000, 4: 45-60.
38. Modular decomposition of protein-protein interaction networks. Supplementary material. [http://www.mas.ecp.fr/labo/equipe/gagneur/module/module.html]