Detecting functional modules in the yeast protein-protein interaction network

Bioinformatics

Volumn 22, Issue 18, 2006, Pages 2283-2290

  Chen, Jingchun ^a   Yuan, Bo ^a  

^a OHIO STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEOME; SACCHAROMYCES CEREVISIAE PROTEIN;

ALGORITHM; ARTICLE; CELL FUNCTION; CONTROLLED STUDY; MICROARRAY ANALYSIS; NONHUMAN; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN FUNCTION; PROTEIN INTERACTION; PROTEIN LOCALIZATION; PROTEOMICS; SACCHAROMYCES CEREVISIAE; VALIDATION PROCESS;

EID: 33748701649     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/btl370     Document Type: Article

References (33)

1. Asakawa,H. et al. (2005) Dissociation of the nuf2-ndc80 complex releases centromeres from the spindle-pole body during meiotic prophase in fission yeast. Mol. Biol. Cell., 16, 2325-2338.
2. Bader,J.S. et al. (2004) Gaining confidence in high-throughput protein interaction networks. Nat. Biotechnol., 22, 78-85.
3. Ball,C.A. et al. (2005) The stanford microarray database accommodates additional microarray platforms and data formats. Nucleic Acids Res., 33, D580-D582.
4. Barabasi,A.L. and Oltvai,Z.N. (2004) Network biology: Understanding the cell's functional organization. Nature Rev. Genet., 5, 101-113.
5. Barrat,A. et al. (2004) The architecture of complex weighted networks. Proc. Natl. Acad. Sci. USA, 101, 3747-3752.
6. Bentley,D.R. (2000) The human genome project-an overview. Med. Res. Rev., 20, 189-196.
7. Berg,J. and Lassig,M. (2004) Local graph alignment and motif search in biological networks. Proc. Natl. Acad. Sci. USA, 101, 14689-14694.
8. Bork,P. et al. (2004) Protein interaction networks from yeast to human. Curr. Opin. Struct. Biol., 14, 292-299.
9. Gartner,W. et al. (2003) The ATP-dependent helicase RUVBL1/TIP49a associates with tubulin during mitosis. Cell. Motil. Cytoskeleton., 56, 79-93.
10. Giaever,G. et al. (2002) Functional profiling of the Saccharomyces cerevisiae genome. Nature, 418, 387-391.
11. Gingras,A.C. et al. (2005) Advances in protein complex analysis using mass spectrometry. J. Physiol., 563, 11-21.
12. Girvan,M. and Newman,M.E. (2002) Community structure in social and biological networks. Proc. Natl. Acad. Sci. USA, 99, 7821-7826.
13. Gunsalus,K.C. et al. (2005) Predictive models of molecular machines involved in Caenorhabditis elegans early embryogenesis. Nature, 436, 861-865.
14. Hartwell,L.H. et al. (1999) From molecular to modular cell biology. Nature, 402, C47-C52.
15. Ho,Y. et al. (2002) Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature, 415, 180-183.
16. Ihmels,J. et al. (2002) Revealing modular organization in the yeast transcriptional network. Nature Genet., 31, 370-377.
17. Ito,T. et al. (2001) A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc. Natl. Acad. Sci. USA, 98, 4569-4574.
18. Newman,M.E. (2001) Scientific collaboration networks II. Shortest paths, weighted networks, and centrality. Phys. Rev. E Stat. Nonlin. Soft. Matter Phys., 64, 016132.
19. Patil,A. and Nakamura,H. (2005) Filtering high-throughput protein-protein interaction data using a combination of genomic features. BMC Bioinformatics, 6, 100.
20. Pereira-Leal,J.B. et al. (2004) Detection of functional modules from protein interaction networks. Proteins, 54, 49-57.
21. Radicchi,F. et al. (2004) Defining and identifying communities in networks. Proc. Natl. Acad. Sci. USA, 101, 2658-2663.
22. Rives,A.W. and Galitski,T. (2003) Modular organization of cellular networks. Proc. Natl. Acad. Sci. USA, 100, 1128-1133.
23. Sanjuan,R. and Marin,I. (2001) Tracing the origin of the compensasome: Evolutionary history of DEAH helicase and MYST acetyltransferase gene families. Mol. Biol. Evol., 18, 330-343.
24. Schlegel,B.P. et al. (2003) Overexpression of a protein fragment of rna helicase a causes inhibition of endogenous brca1 function and defects in ploidy and cytokinesis in mammary epithelial cells. Oncogene, 22, 983-991.
25. Spirin,V. and Mirny,L.A. (2003) Protein complexes and functional modules in molecular networks. Proc. Natl. Acad. Sci. USA, 100, 12123-12128.
26. Tanay,A. et al. (2004) Revealing modularity and organization in the yeast molecular network by integrated analysis of highly heterogeneous genome wide data. Proc. Natl. Acad. Sci. USA, 101, 2981-2986.
27. Troyanskaya,O.G. (2005) Putting microarrays in a context: Integrated analysis of diverse biological data. Brief. Bioinform., 6, 34-43.
28. Uetz,P. et al. (2000) A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature, 403, 623-627.
29. von Mering,C. et al. (2002) Comparative assessment of large-scale data sets of proteinprotein interactions. Nature, 417, 399-403.
30. Wei,R.R. et al. (2005) Molecular organization of the ndc80 complex, an essential kinetochore component. Proc. Natl. Acad. Sci. USA, 102, 5363-5367.
31. Westermann,S. et al. (2005) Formation of a dynamic kinetochore- microtubule interface through assembly of the dam1 ring complex. Mol. Cell., 17, 277-290.
32. Westermann,S. et al. (2006) The dam1 kinetochore ring complex moves processively on depolymerizing microtubule ends. Nature, 440, 565-569.
33. Xiong,H. et al. (2005) Identification of functional modules in protein complexes via hyperclique pattern discovery. Pac. Symp. Biocomput., 221-232.