Discovering functional interaction patterns in protein-protein interaction networks

BMC Bioinformatics

Volumn 9, Issue , 2008, Pages

  Turanalp, Mehmet E ^a   Can, Tolga ^a,b  

^a SELCUK UNIVERSITY   (Turkey)

^b MIDDLE EAST TECHNICAL UNIVERSITY   (Turkey)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL NETWORKS; FUNCTIONAL ANNOTATION; FUNCTIONAL INTERACTION; IDENTIFICATION METHOD; MODULAR ORGANIZATIONS; PATTERN IDENTIFICATION; PHYSICAL INTERACTIONS; PROTEIN-PROTEIN INTERACTION NETWORKS;

BIOLOGY; TOPOLOGY; YEAST;

PROTEINS;

LIGASE; MITOGEN ACTIVATED PROTEIN KINASE; PHOSPHOTRANSFERASE; REGULATOR PROTEIN; SACCHAROMYCES CEREVISIAE PROTEIN; SNARE PROTEIN; TRANSFERASE; PROTEOME;

ALGORITHM; ARTICLE; AUTOMATED PATTERN RECOGNITION; CLUSTER ANALYSIS; COMPLEX FORMATION; COMPUTER PROGRAM; CONTROLLED STUDY; ENZYME REGULATION; FREQUENCY ANALYSIS; LINEAR SYSTEM; NONHUMAN; PROTEIN BINDING; PROTEIN FUNCTION; PROTEIN PROTEIN INTERACTION; PROTEIN TRANSPORT; SACCHAROMYCES CEREVISIAE; SCORING SYSTEM; SIGNAL TRANSDUCTION; ARTIFICIAL INTELLIGENCE; BIOLOGICAL MODEL; COMPUTER SIMULATION; METABOLISM; METHODOLOGY; PHYSIOLOGY; PROTEIN ANALYSIS;

SACCHAROMYCES CEREVISIAE;

ALGORITHMS; ARTIFICIAL INTELLIGENCE; COMPUTER SIMULATION; MODELS, BIOLOGICAL; PATTERN RECOGNITION, AUTOMATED; PROTEIN INTERACTION MAPPING; PROTEOME; SIGNAL TRANSDUCTION;

EID: 46749134436     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-9-276     Document Type: Article

References (54)

1. Uetz P Giot L Cagney G Mansfield TA Judson RS Knight JR Lockshon D Narayan V Srinivasan M Pochart P Qureshi-Emili A Li Y Godwin B Conover D Kalbfleisch T Vijayadamodar G Yang M Johnston M Fields S Rothberg JM A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae Nature 2000, 403:623-627. 10688190
2. Ito T Chiba T Ozawa R Yoshida M Hattori M Sakaki Y A comprehensive two-hybrid analysis to explore the yeast protein interactome Proceedings of the National Academy of Sciences 2001, 98(8):4569-4574.
3. Gavin A Bosche M Krause R Grandi P Marzioch M Bauer A Schultz J Rick J Michon A Cruciat C Remor M Höfert C Schelder M Brajenovic M Ruffner H Merino A Klein K Hudak M Dickson D Rudi T Gnau V Bauch A Bastuck S Huhse B Leutwein C Heurtier M Copley R Edelmann A Querfurth E Rybin V Drewes G Raida M Bouwmeester T Bork P Seraphin B Kuster B Neubauer G Superti-Furga G Functional organization of the yeast proteome by systematic analysis of protein complexes Nature 2002, 415(6868):141-7. 11805826
4. Ho Y Gruhler A Heilbut A Bader GD Moore L Adams SL Millar A Taylor P Bennett K Boutilier K Yang L Wolting C Donaldson I Schandorff S Shewnarane J Vo M Taggart J Goudreault M Muskat B Alfarano C Dewar D Lin Z Michalickova K Willems AR Sassi H Nielsen PA Rasmussen KJ Andersen JR Johansen LE Hansen LH Jespersen H Podtelejnikov A Nielsen E Crawford J Poulsen V Sørensen BD Matthiesen J Hendrickson RC Gleeson F Pawson T Moran MF Durocher D Mann M Hogue CWV Figeys D Tyers M Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry Nature 2002, 415:180-183. 11805837
5. von Mering C Krause R Snel B Cornell M Oliver SG Fields S Bork P Comparative assessment of large-scale data sets of protein-protein interactions Nature 2002, 417:399-403. 12000970
6. Jansen R Yu H Greenbaum D Kluger Y Krogan NJ Chung S Emili A Snyder M Greenblatt JF Gerstein M A bayesian networks approach for predicting protein-protein interactions from genomic data Science 2003, 302(5644):449-453. 14564010
7. Lee I Date SV Adai AT Marcotte EM A probabilistic functional network of yeast genes Science 2004, 306(5701):1555-1558. 15567862
8. Przulj N Wigle D Jurisica I Functional topology in a network of protein interactions Bioinformatics 2004, 20(3):340-348. 14960460
9. Valente AXCN Cusick ME Yeast Protein Interactome topology provides framework for coordinated-functionality Nucl Acids Res 2006, 34(9):2812-2819. 1464412 16717286
10. Luo F Yang Y Chen CF Chang R Zhou J Scheuermann RH Modular organization of protein interaction networks Bioinformatics 2007, 23(2):207-214. 17092991
11. Sharan R Suthram S Kelley RM Kuhn T McCuine S Uetz P Sittler T Karp RM Ideker T From the Cover: Conserved patterns of protein interaction in multiple species Proceedings of the National Academy of Sciences 2005, 102(6):1974-1979.
12. Hirsh E Sharan R Identification of conserved protein complexes based on a model of protein network evolution Bioinformatics 2007, 23(2):e170-176. 17237088
13. Bader G Hogue C An automated method for finding molecular complexes in large protein interaction networks BMC Bioinformatics 2003, 4:2. 149346 12525261
14. Spirin V Mirny LA Protein complexes and functional modules in molecular networks Proceedings of the National Academy of Sciences 2003, 100(21):12123-12128.
15. Asthana S King OD Gibbons FD Roth FP Predicting protein complex membership using probabilistic network reliability Genome Res 2004, 14(6):1170-1175. 419795 15140827
16. Scott J Ideker T Karp RM Sharan R Efficient algorithms for detecting signaling pathways in protein interaction networks RECOMB 2005:1-13.
17. Brohee S van Helden J Evaluation of clustering algorithms for protein-protein interaction networks BMC Bioinformatics 2006, 7:488. 1637120 17087821
18. Cakmak A Ozsoyoglu G Mining biological networks for unknown pathways Bioinformatics 2007, 23(20):2775-2783. 17766269
19. Letovsky S Kasif S Predicting protein function from protein/protein interaction data: A probabilistic approach Bioinformatics 2003, 19(Suppl 1):i197-204. 12855458
20. Lanckriet GRG Deng M Cristianini N Jordan MI Noble WS Kernel-based data fusion and its application to protein function prediction in yeast Proceedings of the Pacific Symposium on Biocomputing 2004:300-311.
21. Hu H Yan X Huang Y Han J Zhou XJ Mining coherent dense subgraphs across massive biological networks for functional discovery Bioinformatics 2005, 21(Suppl 1):i213-221. 15961460
22. Patil A Nakamura H Filtering high-throughput protein-protein interaction data using a combination of genomic features BMC Bioinformatics 2005, 6:100. 1127019 15833142
23. Chen J Hsu W Lee ML Ng SK Increasing confidence of protein interactomes using network topological metrics Bioinformatics 2006, 22(16):1998-2004. 16787971
24. Suthram S Shlomi T Ruppin E Sharan R Ideker T A direct comparison of protein interaction confidence assignment schemes BMC Bioinformatics 2006, 7:360. 1550431 16872496
25. Collins SR Kemmeren P Zhao XC Greenblatt JF Spencer F Holstege FC Weissman JS Krogan NJ Toward a comprehensive atlas of the physical interactome of Saccharomyces cerevisiae Mol Cell Proteomics 2007, 6(3):439-450. 17200106
26. Mahdavi M Lin YH False positive reduction in protein-protein interaction predictions using gene ontology annotations BMC Bioinformatics 2007, 8:262. 1941744 17645798
27. Kashtan N Itzkovitz S Milo R Alon U Mfinder tool guide Technical report, Department of Molecular Cell Biology and Computer Science and Applied Mathematics, Weizman Institute of Science, Israel; 2002.
28. Yeger-Lotem E Sattath S Kashtan N Itzkovitz S Milo R Pinter RY Alon U Margalit H Network motifs in integrated cellular networks of transcription-regulation and protein-protein interaction Proceedings of the National Academy of Sciences 2004, 101(16):5934-5939.
29. Inokuchi A Mining generalized substructures from a set of labeled graphs ICDM '04: Proceedings of the Fourth IEEE International Conference on Data Mining (ICDM'04) Washington, DC, USA: IEEE Computer Society 2004:415-418.
30. Nijssen S Kok JN The gaston tool for frequent subgraph mining Electronic Notes in Theoretical Computer Science 2005, 127:77-87.
31. Yan X Han J gSpan: Graph-based substructure pattern mining ICDM '02: Proceedings of the 2002 IEEE International Conference on Data Mining (ICDM'02) Washington, DC, USA: IEEE Computer Society 2002:721.
32. Oyama T Kitano K Satou K Ito T Extraction of knowledge on protein-protein interaction by association rule discovery Bioinformatics 2002, 18(5):705-714. 12050067
33. Besemann C Denton A Yekkirala A Differential association rule mining for the study of protein-protein interaction networks BIOKDD04: 4th Workshop on Data Mining in Bioinformatics (with SIGKDD Conference) 2004:72-80.
34. Koyuturk M Kim Y Subramaniam S Szpankowski W Grama A Detecting conserved interaction patterns in biological networks Journal of Computational Biology 2006, 13(7):1299-1322. 17037960
35. The Gene Ontology Consortium Gene Ontology: Tool for the unification of biology Nature Genet 2000, 25:25-29. 10802651
36. GO slim and subset guide http://www.geneontology.org/GO.slims.shtml
37. Kanehisa M Goto S KEGG: Kyoto Encyclopedia of Genes and Genomes Nucl Acids Res 2000, 28:27-30. 102409 10592173
38. Pandey J Koyuturk M Kim Y Szpankowski W Subramaniam S Grama A Functional annotation of regulatory pathways Bioinformatics 2007, 23(13):i377-386. 17646320
39. Pandey J Koyutürk M Szpankowski W Grama A Annotating pathways of interaction networks Proceedings of the Pacific Symposium on Biocomputing 2008, 13:153-165.
40. Levy ED Pereira-Leal JB Chothia C Teichmann SA 3D complex: A structural classification of protein complexes PLoS Computational Biology 2006, 2(11):e155. 1636673 17112313
41. Bernard A Vaughn DS Hartemink AJ Reconstructing the topology of protein complexes RECOMB, Volume 4453 of Lecture Notes in Computer Science. Springer Speed TP, Huang H 2007:32-46.
42. Koyutürk M Grama A Szpankowski W An efficient algorithm for detecting frequent subgraphs in biological networks Bioinformatics 2004, 20(Suppl 1):200-207. 15262800
43. Kuramochi M Karypis G Finding frequent patterns in a large sparse graph Data Min Knowl Discov 2005, 11(3):243-271.
44. Wernicke S A faster algorithm for detecting network motifs WABI 2005:165-177.
45. You CH Holder LB Cook DJ Application of graph-based data mining to metabolic pathways ICDMW '06: Proceedings of the Sixth IEEE International Conference on Data Mining - Workshops Washington, DC, USA: IEEE Computer Society 2006:169-173.
46. Salwinski L Miller CS Smith AJ Pettit FK Bowie JU Eisenberg D The Database of Interacting Proteins: 2004 update Nucl Acids Res 2004, 32(Suppl 1):D449-451. 14681454 308820
47. Mewes HW Amid C Arnold R Frishman D Guldener U Mannhaupt G Munsterkotter M Pagel P Strack N Stumpflen V Warfsmann J Ruepp A MIPS: Analysis and annotation of proteins from whole genomes Nucleic Acids Research 2004, 32:D41-D44. 308826 14681354
48. Mathivanan S Periaswamy B Gandhi T Kandasamy K Suresh S Mohmood R Ramachandra Y Pandey A An evaluation of human protein-protein interaction data in the public domain BMC Bioinformatics 2006, 7(Suppl 5):S19. 1764475 17254303
49. von Mering C Jensen LJ Kuhn M Chaffron S Doerks T Kruger B Snel B Bork P STRING 7-recent developments in the integration and prediction of protein interactions Nucleic Acids Research 2007, 35(Database):D358-D362. 1669762 17098935
50. Kiemer L Costa S Ueffing M Cesareni G WI-PHI: A weighted yeast interactome enriched for direct physical interactions PROTEOMICS 2007, 7(6):932-943. 17285561
51. Cordella LP Foggia P Sansone C Vento M A (sub)graph isomorphism algorithm for matching large graphs IEEE Trans. Pattern Anal Mach Intell 2004, 6(10):1367-1372.
52. McKay BD Practical graph isomorphism Congressus Numerantium 1981, 30:45-87.
53. Ullmann JR An algorithm for subgraph isomorphism J ACM 1976, 23:31-42.
54. Yan X Han J CloseGraph: Mining closed frequent graph patterns KDD '03: Proceedings of the ninth ACM SIGKDD international conference on Knowledge discovery and data mining New York, NY, USA: ACM 2003:286-295.