Modular organization of protein interaction networks

Bioinformatics

Volumn 23, Issue 2, 2007, Pages 207-214

  Luo, Feng ^a,c   Yang, Yunfeng ^b   Chen, Chin Fu ^c   Chang, Roger ^e   Zhou, Jizhong ^d   Scheuermann, Richard H ^e  

^a AMRL   (United States)

^b OAK RIDGE NATIONAL LABORATORY   (United States)

^c Department of Genetics and Biochemistry ^*  (United States)

^d UNIVERSITY OF OKLAHOMA   (United States)

^e UNIVERSITY OF TEXAS SOUTHWESTERN MEDICAL CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CORE PROTEIN;

ALGORITHM; ARTICLE; CLUSTER ANALYSIS; COMPUTER PROGRAM; DATA ANALYSIS; FUNCTIONAL PROTEOMICS; PRIORITY JOURNAL; PROTEIN DATABASE; PROTEIN INTERACTION;

EID: 33846681448     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/btl562     Document Type: Article

References (27)

1. Arnau,V. et al. (2005) Iterative cluster analysis of protein interaction data. Bioinformatics, 21, 364-378.
2. Bader,G.D. and Hogue,C.W.V. (2003) An automated method for finding molecular complexes in large protein interaction networks. BMC Bioinformatics, 4, 2.
3. Barabasi,A.-L. and Oltvai,Z.N. (2004) Network biology: Understanding the cell's functional organization. Nat. Rev., 5, 101-114.
4. Basso,K. et al. (2005) Reverse engineering of regulatory networks in human B cells. Nat. Genet., 37, 382-390.
5. Batagelj,V. and Mrvar,A. Pajek - Program for large network analysis.
6. Bu,D. et al. (2003) Topological structure analysis of the protein-protein interaction network in budding yeast. Nucleic Acids Res., 31, 2443-2450.
7. Chen,J. and Yuan,B. (2006) Detecting functional modules in the yeast protein-protein interaction network. Bioinformatics, 22, 2283-2290.
8. Cherry,J.M. et al. (1998) SGD: Saccharomyces Genome Database. Nucleic Acids Res., 26, 73-79.
9. Deane,C.M. et al. (2002) Protein interactions: Two methods for assessment of the reliability of high-throughput observations. Mol. Cell. Proteomics, 1, 349-356.
10. Enright,A.J. and Ouzounis,C.A. (2001) BioLayout - an automatic graph layout algorithm for similarity visualization. Bioinformatics, 17, 853-854.
11. Girvan,M. and Newman,M.E. (2002) Community structure in social and biological networks. Proc. Natl Acad. Sci. USA, 99, 7821-7826.
12. Guimera,R. and Amaral,L.A.N. (2005) Functional cartography of complex metabolic networks. Nature, 433, 895-900.
13. Hartwell,L.H. et al. (1999) From molecular to modular cell biology. Nature, 402, C47-C52.
14. Hong,E.L., Balakrishnan,R., Christie,K.R., Costanzo,M.C., Dwight,S.S., Engel,S.R., Fisk,D.G., Hirschman,J.E., Livstone,M.S., Nash,R., Oughtred,R., Park,J., Skrzypek,M., Starr,B., Theesfeld,C.L., Andrada,R., Binkley,G., Dong,Q., Lane,C.D., Hitz,B.C., Miyasato,S., Schroeder,M., Weng,S., Wong,E.D., Dolinski,K., Botstein,D., Cherry,J.M. Saccharomyces Genome Database.
15. MacCuish,J. et al. (2001) Ties in proximity and clustering compounds. J. Chem. Inform. Comp. Sci., 41, 134-146.
16. Newman,M.E.J. (2004) Fast algorithm for detecting community structure in networks. Phys. Rev. E, 69, 066133.
17. Pereira-Leal,J.B. et al. (2004) Detection of functional modules from protein interaction networks. Proteins: Struct. Func. Bioinformatics, 54, 49-57.
18. Qi,Y.J. et al. (2006) Evaluation of different biological data and computational classification methods for use in protein interaction prediction. Proteins: Struct. Func. Bioinformatics, 63, 490-500.
19. Radicchi,F. et al. (2004) Defining and identifying communities in networks. Proc. Natl Acad. Sci. USA, 101, 2658-2663.
20. Ravasz,E. et al. (2002) Hierarchical organization of modularity in metabolic networks. Science, 297, 1551-1555.
21. River,A.W. and Galitski,T. (2003) Modular organization of cellular networks. Proc. Natl Acad. Sci. USA, 100, 1128-1133.
22. Snel,B. et al. (2002) The identification of functional modules from the genomic association of genes. Proc. Natl Acad. Sci. USA, 99, 5890-5895.
23. Spirin,V. and Mirny,L.A. (2003) Protein complexes and functional modules in molecular networks. Proc. Natl Acad. Sci. USA, 100, 12123-12128.
24. Wasserman,S. and Faust,K. (1994) Social Network Analysis. Cambridge University Press, Cambridge, UK.
25. Wilhelm,T. et al. (2003) Physical and functional modularity of the protein network in Yeast. Mol. Cell. Proteomics, 2, 292-298.
26. Xiong,H. et al. (2005) Identification of functional modules in protein complexes via hyperclique pattern discovery. Pac. Symp. Biocomp., 10, 221-232.
27. Xenarios,I. et al. (2002) DIP, the Database of Interacting Proteins: A research tool for studying cellular networks of protein interactions. Nucleic Acids Res., 30, 303-305.