A novel functional module detection algorithm for protein-protein interaction networks

Algorithms for Molecular Biology

Volumn 1, Issue 1, 2006, Pages

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

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

^b UNIVERSITY AT BUFFALO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 34248397539     PISSN: None     EISSN: 17487188     Source Type: Journal    
DOI: 10.1186/1748-7188-1-24     Document Type: Article

References (26)

1. Letovsky S Kasif S Predicting protein function from protein/protein interaction data: A probabilistic approach Bioinformatics 2003 19 i197-i204 10.1093/bioinformatics/btg1026 12855458
2. Gavin AC Functional organization of the yeast proteome by systematic analysis of protein complexes Nature 2002 415 141-147 10.1038/415141a 11805826
3. Ho Y Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry Nature 2002 415 180-183 10.1038/415180a 11805837
4. Ito T A comprehensive two-hybrid analysis to explore the yeast protein interactome PNAS 2001 98 4569-4574 31875 11283351 10.1073/pnas.061034498
5. Uetz P A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae Nature 2000 403 623-627 10.1038/35001009 10688190
6. Hishigaki H Nakai K Ono T Tanigami A Takagi T Assessment of prediction accuracy of protein function from protein-protein interaction data Yeast 2001 18 523-531 10.1002/yea.706 11284008
7. Bu D Topological structure analysis of the protein-protein interaction network in budding yeast Nucleic Acids Res 2003 31 2443-2450 154226 12711690 10.1093/nar/gkg340
8. Guimera R Nunes Amaral L Functional cartography of complex metabolic networks Nature 2005 433 895-900 10.1038/nature03288 15729348
9. Pereira-Leal JB Enright AJ Ouzounis CA Detection of functional modules from protein interaction networks Proteins 2004 54 49-57 10.1002/ prot.10505 14705023
10. Lin C Knowledge Discovery in Bioinformatics: Techniques, Methods, and Applications John Wiley & Sons Inc. chap. Clustering methods in protein-protein interaction network 2006
11. Spirin V Mirny LA Protein complexes and functional modules in molecular networks PNAS 2003 100 12123-12128 218723 14517352 10.1073/ pnas.2032324100
12. Bader GD Hogue CW 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
13. King AD Przulj N Jurisica I Protein complex prediction via cost-based clustering Bioinformatics 2004 20 3013-3020 10.1093/bioinformatics/ bth351 15180928
14. Hartuv E Shamir R A Clustering Algorithm based Graph Connectivity Information Processing Letters 2000 76 175-181 10.1016/ S0020-0190(00)00142-3
15. van Dongen S Technical Report INS-R0010: A cluster algorithm for graphs National Research Institute for Mathematics and Computer Science 2000
16. Samanta MP Liang S Predicting protein functions from redundancies in large-scale protein interaction networks PNAS 2003 100 12579-12583 240660 14566057 10.1073/pnas.2132527100
17. Mewes HW MIPS: Analysis and annotation of proteins from whole genome in 2005 Nucleic Acid Research 2006 34 D169-D172 10.1093/nar/gkj148
18. Johnson NL Kotz S Balakrishnan N Continuous univariate distributions John Wiley & sons, New York, NY 1994
19. Ramanathan M A dispersion model for cellular signal transduction cascades Pharm Res 2002 19 1544-1548 10.1023/A:1020421119533 12425474
20. Hallett MB Pettit EJ Stochastic events underlie Ca2+ signalling in neutrophils J Theor Biol 1997 186 1-6 10.1006/ jtbi.1996.0345 9176633
21. Dennis B Patil GP The gamma distribution and weighted multimodal gamma distributions as models of population abundance Math Biosciences 1984 68 187-212 10.1016/0025-5564(84)90031-2
22. Deane CM Salwinski L Xenarios I Eisenberg D Protein interactions: Two methods for assessment of the reliability of high throughput observations Mol Cell Proteomics 2002 1 349-356 10.1074/ mcp.M100037-MCP200 12118076
23. Samanta MP Liang S Redundancies in large-scale protein interaction networks Proc Natl Acad Sci 2003 100 12579-12583 240660 14566057 10.1073/ pnas.2132527100
24. Girvan M Newman MEJ Community structure in social and biological networks PNAS 2002 99 7821-7826 122977 12060727 10.1073/pnas.122653799
25. Johnson DB Efficient algorithms for shortest paths in sparse networks J of the ACM 1977 24 1-13 10.1145/321992.321993
26. Karypis G Han E-H Kumar V Chameleon: Hierarchical clustering using dynamic modeling IEEE Computer: Special issue on data analysis and mining 1999 32 68-75