Semantic integration to identify overlapping functional modules in protein interaction networks

BMC Bioinformatics

Volumn 8, Issue , 2007, Pages

  Cho, Young Rae ^a   Hwang, Woochang ^a   Ramanathan, Murali ^b   Zhang, Aidong ^a  

^a the State University of New York   (United States)

^b UNIVERSITY AT BUFFALO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CELLULAR ORGANIZATION; FUNCTIONAL MODULE DETECTIONS; INTERACTION NETWORKS; MODULE IDENTIFICATIONS; PROTEIN INTERACTION NETWORKS; PROTEIN-PROTEIN INTERACTIONS; SEMANTIC INTEGRATION; SEMANTIC SIMILARITY;

ACTIVE NETWORKS; ALGORITHMS; COMPLEX NETWORKS; DATA INTEGRATION; INTEGRATION; MODULAR CONSTRUCTION; PROTEINS; SEMANTICS;

INTEGRAL EQUATIONS;

SACCHAROMYCES CEREVISIAE PROTEIN; PROTEOME;

ACCURACY; ALGORITHM; ARTICLE; BIOINFORMATICS; FUNCTIONAL PROTEOMICS; NONHUMAN; PROTEIN ANALYSIS; PROTEIN DATABASE; PROTEIN FUNCTION; PROTEIN PROTEIN INTERACTION; RELIABILITY; SACCHAROMYCES CEREVISIAE; SEMANTIC DIFFERENTIAL METHOD; BIOLOGICAL MODEL; COMPUTER SIMULATION; INFORMATION RETRIEVAL; METABOLISM; METHODOLOGY; NATURAL LANGUAGE PROCESSING; PHYSIOLOGY; SEMANTICS; SIGNAL TRANSDUCTION; SYSTEM ANALYSIS;

ALGORITHMS; COMPUTER SIMULATION; DATABASES, PROTEIN; INFORMATION STORAGE AND RETRIEVAL; MODELS, BIOLOGICAL; NATURAL LANGUAGE PROCESSING; PROTEIN INTERACTION MAPPING; PROTEOME; SEMANTICS; SIGNAL TRANSDUCTION; SYSTEMS INTEGRATION;

EID: 34548511546     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-8-265     Document Type: Article

References (40)

1. Hartwell LH Hopfield JJ Leibler S Murray AW From molecular to modular cell biology Nature 1999 402 c47-c52 10591225
2. Uetz P A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae Nature 2000 403 623-627 10688190
3. Ito T A comprehensive two-hybrid analysis to explore the yeast protein interactome PNAS 2001 98 8 4569-4574 31875 11283351
4. Gavin A-C Functional organization of the yeast proteome by systematic analysis of protein complexes Nature 2002 415 141-147 11805826
5. Ho Y Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry Nature 2002 415 180-183 11805837
6. von Mering C Comparative assessment of large-scale data sets of protein-protein interactions Nature 2002 417 399-403 12000970
7. Cho Y-R Hwang W Zhang A Identification of overlapping functional modules in protein interaction networks: Information flow-based approach Proceedings of 6th IEEE International Conference on Data Mining -Workshops 2006 147-152
8. Ideker T Ozier O Schwikowski B Siegel AF Discovering regulatory and signalling circuits in molecular interaction networks Bioinformatics 2002 18 S233-S240 12169552
9. Tornow S Mewes HW Functional modules by relating protein interaction networks and gene expression Nucleic Acids Res 2003 31 21 6283-6289 275479 14576317
10. The Gene Ontology Consortium The Gene Ontology (GO) project in 2006 Nucleic Acids Research 2006 34 D322-326 1347384 16381878
11. Hvidsten TR Lagreid A Komorowski J Learning rule-based models of biological process from gene expression time profiles using Gene Ontology Bioinformatics 2003 19 9 1116-1123 12801872
12. Fang Z Yang J Li Y Luo Q Liu L Knowledge guided analysis of microarray data Journal of Biomedical Informatics 2006 39 401-411 16214421
13. Doherty JM Carmichael LK Mills JC GOurmet: A tool for quantitative comparison and visualization of gene expression profiles based on gene ontology (GO) distributions BMC Bioinformatics 2006 7 151 1459206 16545118
14. Barrat A Barthelemy M Pastor-Satorras R Vespignani A The architecture of complex weighted netowrks PNAS 2004 101 11 3747-3752 374315 15007165
15. Lubovac Z Gamalielsson J Olsson B Combining functional and topological properties to identify core modules in protein interaction networks PROTEINS: Structure, Function, and Bioinformatics 2006 64 4 948-959
16. Spirin V Mirny LA Protein complexes and functional modules in molecular networks PNAS 2003 100 21 12123-12128 218723 14517352
17. Bu D Topological structure analysis of the protein-protein interaction network in budding yeast Nucleic Acid Research 2003 31 9 2443-2450
18. Bader GD Hogue CW An automated method for finding molecular complexes in large protein interaction networks BMC Bioinformatics 2003 4 2
19. Brun C Herrmann C Guenoche A Clustering proteins from interaction networks for the prediction of cellular functions BMC Bioinformatics 2004 5 95 487898 15251039
20. Altaf-Ul-Amin M Shinbo Y Mihara K Kurokawa K Kanaya S Development and implementation of an algorithm for detection of protein complexes in large interaction networks BMC Bioinformatics 2006 7 207 1473204 16613608
21. Pei P Zhang A A "seed-refine" algorithm for detecting protein complexes from protein interaction data IEEE Transactions on Nanobioscience 2007 6 1 43-50 17393849
22. Palla G Derenyi I Farkas I Vicsek T Uncovering the overlapping community structure of complex networks in nature and society Nature 2005 435 814-818 15944704
23. Zotenko E Guimaraes KS Jothi R Przytycka TM Decomposition of overlapping protein complexes: A graph theoretical method for analyzing static and dynamic protein associations Algorithms for Molecular Biology 2006 1 7 1481596 16722537
24. Barabási A-L Oltvai ZN Network biology: Understanding the cell's functional organization Nature Reviews: Genetics 2004 5 101-113 14735121
25. King AD Przulj N Jurisica I Protein complex prediction via cost-based clustering Bioinformatics 2004 20 17 3013-3020 15180928
26. Ravasz E Somera AL Mongru DA Oltvai ZN Barabási A-L Hierarchical organization of modularity in metabolic networks Science 2002 297 1551-1555 12202830
27. Tanay A Sharan R Kupiec M Shamir R Revealing modularity and organization in the yeast molecular network by integrated analysis of highly heterogeneous genomewide data PNAS 2004 101 9 2981-2986 365731 14973197
28. Rives AW Galitski T Modular organization of cellular networks PNAS 2003 100 3 1128-1133 298738 12538875
29. Samanta MP Liang S Predicting protein functions from redundancies in large-scale protein interaction networks PNAS 2003 100 22 12579-12583 240660 14566057
30. Arnau V Mars S Marin I Iterative cluster analysis of protein interaction data Bioinformatics 2005 21 3 364-378 15374873
31. Tetko IV Facius A Ruepp A Mewes HW Super paramagnetic clustering of protein sequences BMC Bioinformatics 2005 6 82 1084344 15804359
32. Girvan M Newman MEJ Community structure in social and biological networks PNAS 2002 99 12 7821-7826 122977 12060727
33. Dunn R Dudbridge F Sanderson CM The use of edge-betweenness clustering to investigate biological function in protein interaction networks BMC Bioinformatics 2005 6 555937 15740614
34. Hwang W Cho Y-R Zhang A Ramanathan M A novel functional module detection algorithm for protein-protein interaction networks Algorithms for Molecular Biology 2006 1 24 1764415 17147822
35. Resnik P Using information content to evaluate semantic similarity in a taxonomy Proceedings of 14th International Joint Conference on Artificial Intelligence 1995 448-453
36. Salwinski L The database of interacting proteins: 2004 update Nucleic Acid Research 2004 32 D449-D451
37. Mewes HW MIPS: Analysis and annotation of proteins from whole genome in 2005 Nucleic Acid Research 2006 34 D169-D172
38. Jeong H Mason SP Barabási A-L Oltvai ZN Lethality and centrality in protein networks Nature 2001 411 41-42 11333967
39. Deane CM Salwinski L Xenarios I Eisenberg D Protein interactions: Two methods for assessment of the reliability of high throughput observations Molecular and Cellular Proteomics 2002 1 5 349-356
40. Ball CA The Stanford Microarray Database accommodates additional microarray platforms and data formats Nucleic Acid Research 2005 33 Database issue D580-D582