The use of edge-betweenness clustering to investigate biological function in protein interaction networks

BMC Bioinformatics

Volumn 6, Issue , 2005, Pages

  Dunn, Ruth ^a   Dudbridge, Frank ^b   Sanderson, Christopher M ^c  

^a WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^b UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^c MRC Rosalind Franklin Centre for Genomics Research   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL FUNCTIONS; FREELY AVAILABLE SOFTWARE; FUNCTIONAL ANNOTATION; GENE ONTOLOGY TERMS; PROTEIN ANNOTATION; PROTEIN INTERACTION; PROTEIN INTERACTION NETWORKS; STATISTICAL PACKAGES;

ACTIVE NETWORKS;

PROTEINS;

ALGORITHM; ANALYTICAL ERROR; ARTICLE; AUTOMATION; BIOINFORMATICS; CELL METABOLISM; CLUSTER ANALYSIS; COMPUTER PROGRAM; CONTROLLED STUDY; CORRELATION ANALYSIS; INFORMATION PROCESSING; NONHUMAN; PROTEIN ANALYSIS; PROTEIN INTERACTION; BIOLOGICAL MODEL; BIOLOGY; CHEMISTRY; COMPUTER LANGUAGE; GENETIC TRANSCRIPTION; GENOMICS; HUMAN; HUMAN GENOME; LABORATORY DIAGNOSIS; PROCEDURES; PROTEIN DATABASE; PROTEOMICS; SOFTWARE;

PROTEIN;

ALGORITHMS; CLUSTER ANALYSIS; COMPUTATIONAL BIOLOGY; DATABASES, PROTEIN; FALSE POSITIVE REACTIONS; GENOME, HUMAN; GENOMICS; HUMANS; MODELS, BIOLOGICAL; PROGRAMMING LANGUAGES; PROTEIN INTERACTION MAPPING; PROTEINS; PROTEOMICS; SOFTWARE; TRANSCRIPTION, GENETIC;

EID: 25444490121     PISSN: 14712105     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-6-39     Document Type: Article

References (32)

1. Bader JS, Chaudhuri A, Rothberg JM, Chant J: Gaining Confidence in High-throughput Protein Interaction Networks. Nature Biotechnology 2004, 22:78-85.
2. 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.
3. Giot L, Bader JS, Brouwer C, Chaudhuri A, Kuang B, Li Y, Hao YL, Ooi CE, Godwin B, Vitols E, Vijayadamodar G, Pochart P, Machineni H, Welsh M, Kong Y, Zerhusen B, Malcolm R, Varrone Z, Collis A, Minto M, Burgess S, McDaniel L, Stimpson E, Spriggs F, Williams J, Neurath K, Ioime N, Agee M, Voss E, Furtak K, Renzulli R, Aanensen N, Carrolla S, Bickelhaupt E, Lazovatsky Y, DaSilva A, Zhong J, Stanyon CA Jr RLF, White KP, Braverman M, Jarvie T, Gold S, Leach M, Knight J, Shimkets RA, McKenna MP, Chant J, Rothberg JM: A Protein Interaction Map of Drosophila melanogaster. Science 2003, 302:1727-1736.
4. Spirin V, Mirny LA: Protein Complexes and Functional Modules in Molecular Networks. Proc Natl Acad Sci USA 2003, 100(21):12123-12126.
5. Girvan M, Newman MEJ: Community Structure in Social and Biological Networks. Proc Natl Acad Sci USA 2002, 99:7821-7826.
6. Newman MEJ: Detecting Community Structure in Networks. Eur Phys J B 2004, 38:321-330.
7. Holme P, Huss M, Jeong H: Subnetwork Hierarchies of Biochemical Pathways. Bioinformatics 2003, 19(4):532-538.
8. Brun C, Herrmann C, Guenoche A: Clustering Proteins from Interaction Networks for the Prediction of Cellular Functions. BMC Bioinformatics 2004, 5:95.
9. Bader GD, Hogue CWV: An Automated Method for Finding Molecular Complexes in Large Protein Interaction Networks. BMC Bioinformatics 2003, 4:2.
10. Pereira-Leal JB, Enright AJ, Ouzounis CA: Detection of Functional Modules from Protein Interaction Networks. Proteins 2004, 54:49-57.
11. Bader GD, Enright AJ: Intermolecular Interactions and Biological Pathways. In Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins 3rd edition. Edited by: Baxevanis A, Ouellette B. pub Wiley; 2004.
12. Lehner B, Semple JI, Brown SE, Counsell D, Campbell RD, Sanderson CM: Analysis of a High-throughput Yeast Two-hybrid System and its Use to Predict the Function of Intracellular Proteins Encoded within the Human MHC Class III Region. Genomics 2004, 83:153-167.
13. Lehner B, Sanderson CM: A Protein Interaction Framework for Human and mRNA Degradation. Genome Research 2004, 14(7):1315-1323.
14. Uetz P, Giot L, Cagney G, Mansfeld 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, 403:623-631.
15. Gavin AC, Bosche M, Krause R, Grandi P, Marzioch M, Bauer A, Schultz J, Rick JM, Michon AM, Cruciat CM, Remor M, Hofert 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 MA, Copley RR, Edelmann A, Querfurth E, Rybin V, Drewes G, Raida M, Bouwmeester T, Bork P, Seraphin B, Kuster B, Neubauer G, Superti-Furga G: Functional Organisation of the Yeast Proteome by Systematic Analysis of Protein Complexes. Nature 2002, 415:141-147.
16. Newman MEJ, Girvan M: Finding and Evaluating Community Structure in Networks. Phys Rev E 2004, 69:026113.
17. JUNG API Documentation [http://jung.sourceforge.net/doc/api/index.html]
18. 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.
19. Gene Ontology: Tool for the unification of biology. Nature Genetics 2000, 25:25-29.
20. GraphML [http://graphml.graphdrawing.org/]
21. JUNG: Java Universal Network/Graph Framework [http://jung.sourceforge.net]
22. Pruitt KD, Tatusova T, Maglott DR: NCBI Reference Sequence project: update and current status. Nucleic Acids Res 2003, 31:34-7.
23. Bader GD, Betel D, Hogue CW: Nucleic Acids Research 2003, 31:248-50.
24. GO term database [http://www.godatabase.org/dev/database/archive]
25. PostgreSQL Database Management System [http://www.postgresql.org]
26. GO database queries [http://www.godatabase.org/dev/sql/doc/example-queries.html]
27. R statistical package [http://www.r-project.org]
28. BIND [http://bind.ca]
29. Breitkreutz BJ, Stark C, Tyers M: Osprey: A Network Visualization System. Genome Biology 2003, 4(3):R22.
30. Osprey [http://biodata.mshri.on.ca/osprey/servlet/Index]
31. IntAct [http://www.ebi.ac.uk/intact]
32. BioLayout [http://maine.ebi.ac.uk:8000/services/biolayout/]