Decomposition of overlapping protein complexes: A graph theoretical method for analyzing static and dynamic protein associations

Algorithms for Molecular Biology

Volumn 1, Issue 1, 2006, Pages

  Zotenko, Elena ^a,b   Guimarães, Katia S ^a,c   Jothi, Raja ^a   Przytycka, Teresa M ^a  

^a NATIONAL INSTITUTES OF HEALTH   (United States)

^b University of Maryland ^*  (United States)

^c FEDERAL UNIVERSITY OF PERNAMBUCO   (Brazil)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 34248396293     PISSN: None     EISSN: 17487188     Source Type: Journal    
DOI: 10.1186/1748-7188-1-7     Document Type: Article

References (27)

1. Uetz P Giot L Cagney G Mansfield T Judson R Knight J Lockshon D Narayan V Srinivasan M Pochart P A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae Nature 2000 403 623-627 10688190 10.1038/35001009
2. 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 U S A 2001 98 4569-74 10.1073/pnas.061034498 11283351 31875
3. Ho Y Gruhler A Heilbut A Bader G Moore L Adams S Millar A Taylor P Bennett K Boutilier K Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry Nature 2002 415 180-183 10.1038/415180a 11805837
4. Gavin A Bosche M Krause R Grandi P Marzioch M Bauer A Schultz J Rick J Michon A Cruciat C Functional organization of the yeast proteome by systematic analysis of protein complexes Nature 2002 415 141-147 10.1038/ 415141a 11805826
5. Bouwmeester T Bauch A Ruffner H Angrand P Bergamini G Croughton K Cruciat C Eberhard D Gagneur J Ghidelli S A physical and functional map of the human TNF-alpha/NF-kappaB signal transduction pathway Nature Cell Biology 2004 6 97-105 10.1038/ncb1086 14743216
6. Barabasi A Albert R Emergence of scaling in random networks Science 1999 286 509-512 10.1126/science.286.5439.509 10521342
7. Przulj N Corneil D Jurisica I Modeling interactome: Scale-free or geometric? Bioinformatics 2004 20 18 3508-3515 10.1093/bioinformatics/ bth436 15284103
8. Przytycka T Yu Y Scale-free networks versus evolutionary drift Comput Biol Chem 2004 28 257-264 10.1016/j.compbiolchem.2004.07.001 15548452
9. Hartwell LH Hopfield JJ Leibler S Murray AW From molecular to modular cell biology Nature 1999 402 C47-C52 10.1038/35011540 10591225
10. Bader G Hogue C An automated method for finding molecular complexes in large protein interaction networks BMC Bioinformatics 2003 4 2 149346 12525261 10.1186/1471-2105-4-2
11. Rives A Galitski T Modular organization of cellular networks Proc Natl Acad Sci U S A 2003 100 1128-33 10.1073/pnas.0237338100 12538875 298738
12. Bu D Zhao Y Cai L Xue H Zhu X Lu H Zhang J Sun S Ling L Zhang N Li G Chen R Topological structure analysis of the protein-protein interaction network in budding yeast Nucleic Acids Research 2003 31 9 2443-2450 154226 12711690 10.1093/nar/gkg340
13. Spirin V Mirny L Protein complexes and functional modules in molecular networks Proc Natl Acad Sci U S A 2003 100 12123-12128 10.1073/ pnas.2032324100 14517352 218723
14. Steffen M Petti A Aach J D'haeseleer P Church G Automated modelling of signal transduction networks BMC Bioinformatics 2002 3 34 137599 12413400 10.1186/1471-2105-3-34
15. Tornow S Mewes HW Functional modules by relating protein interaction networks and gene expression Nucleic Acids Research 2003 31 6283 6289-275479 14576317 10.1093/nar/gkg838
16. Gagneur J Krause R Bouwmeester T Casari G Modular decomposition of protein-protein interaction networks Genome Biology 2004 5 8 R57 507882 15287979 10.1186/gb-2004-5-8-r57
17. Gavril F The intersection graphs of subtrees in trees are exactly the chordal graphs Journal of Combinatorial Theory (B) 1974 16 47-56 10.1016/ 0095-8956(74)90094-X
18. Golumbic MC Algorithmic Graph Theory and Perfect Graphs Academic Press, New York 1980
19. Shamir R Advanced topics in graph theory Tech rep Tel-Aviv University 1994
20. Corneil D Perl Y Stewart L Complement reducible graphs Discrete Applied Mathematics 1981 3 163-174 10.1016/0166-218X(81)90013-5
21. Mewes H Frishman D Guldener U Mannhaupt G Mayer K Mokrejs M Morgenstern B Munsterkotter M Rudd S Weil B MIPS: A database for genomes and protein sequences Nucleic Acids Research 2002 30 31-34 99165 11752246 10.1093/ nar/30.1.31
22. Wang Y Dohlman H Pheromone signaling mechanisms in yeast: A prototypical sex machine Science 2004 306 5701 1508-1509 10.1126/science.1104568 15567849
23. Irie K Takase M Lee K Levin D Araki H Matsumoto K Oshima Y MKK1 and MKK2, which encode Saccharomyces cerevisiae mitogen-activated protein kinase-kinase homologs, function in the pathway mediated by protein kinase C Mol Cell Biol 1993 13 3076-3083 359700 8386320
24. Elion E Qi M Chen W SIGNAL TRANSDUCTION: Signaling Specificity in Yeast Science 2005 307 5710 687-688 10.1126/science.1109500 15692041
25. Ho C Lee R Counting clique trees and computing perfect elimination schemes in parallel Information Processing Letters 1989 31 61-68 10.1016/ 0020-0190(89)90070-7
26. Downey R Fellows M Parametrized Complexity Springer-Verlag 1997
27. Batagelj V Mrvar A Pajek - Program for large network analysis Connections 1998 2 47-57