Structure discovery in PPI networks using pattern-based network decomposition

Bioinformatics

Volumn 25, Issue 14, 2009, Pages 1814-1821

  Bachman, Philip ^a   Liu, Ying ^a,b  

^a The University of Texas at Dallas   (United States)

^b UNIVERSITY OF TEXAS AT DALLAS   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ARTICLE; COMPUTER GRAPHICS; CONTROLLED STUDY; INFORMATION PROCESSING; PRIORITY JOURNAL; PROTEIN DATABASE; PROTEIN PROTEIN INTERACTION; SACCHAROMYCES CEREVISIAE; STATISTICAL ANALYSIS; STRUCTURE ANALYSIS;

ALGORITHMS; COMPUTATIONAL BIOLOGY; PROTEIN INTERACTION MAPPING; SACCHAROMYCES CEREVISIAE PROTEINS;

SACCHAROMYCES CEREVISIAE;

EID: 67649866312     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btp297     Document Type: Article

References (35)

1. Aebersold,R. and Mann,M. (2003) Mass spectrometry-based proteomics. Nature, 422, 198-207.
2. Albert,R. et al. (2000) Error and attack tolerance of complex networks. Nature, 406, 378-381.
3. Babai,L. and Luks,E.M. (1983) Canonical labeling of graphs. In Proceedings of the fifteenth annual ACM symposium on Theory of computing Boston, MA, USA, pp. 171-183.
4. Bader,G.D. and Hogue,C.W. (2002) Analyzing yeast protein-protein interaction data obtained from different sources. Nat. Biotechnol. 20, 991-997.
5. Bader,G.D. and Hogue,C.W. (2003) An automated method for finding molecular complexes in large protein networks. BMC Bioinformatics, 4, 2.
6. Chen,J. et al. (2006) Nemofinder: Dissecting genome-wide protein-protein interactions with meso-scale network motifs. In Proceedings of the 12th ACM SIGKDD International Conference on Knowledge Discovery and Datamining. Philadelphia, PA, USA, pp. 106-115.
7. Cordella,L.P. et al. (2001) An improved algorithm for matching large graphs. In Proceedings of the 3rd IAPR-TC15 Workshop on Graph-based Representations in Pattern Recognition, Cuen. Ischia, Italy, pp. 149-159.
8. Enright,A.J. et al. (2002) An efficient algorithm for large-scale detection of protein families. Nucleic Acids Res., 30, 1575-1584.
9. Fields,S. (2005) High-throughput two-hybrid analysis: The promise and the peril. FEBS J., 272, 5391-5399.
10. Grochow,J.A. and Kellis,M. (2007) Network motif discovery using subgraph enumeration and symmetry-breaking. In Proceedings of the 11th Annual International Conference on Research in Computational Molecular Biology, RECOMB 2007. Oakland, CA, USA, pp. 92-106.
11. Guelzim,N. et al. (2002) Topological and causal structure of the yeast transcriptional regulatory network. Nat. Genet., 31, 60-63.
12. Jeong,H. et al. (2000) The large-scale organization of metabolic networks. Nature, 407, 651-654.
13. Kashtan,N. et al. (2004) Topological generalizations of network motifs. Phys. Rev. E, 70, 031909.
14. Lacroix,V. et al. (2006) Motif search in graphs: Application to metabolic networks. IEEE/ACM Trans. Comput. Biol. Bioinform., 3 360-368.
15. McKay,B.D. (1981) Practical graph isomorphism. Congressus Numerantium 30, 45-87.
16. McKay,B.D. (1998) Isomorph-free exhaustive generation. J. Algorithms 26, 306-324.
17. Mewes,H.W. et al (2002) Mips: A database for genomes and protein sequences. Nucleic Acids Res., 30, 31-34.
18. Milo,R. et al. (2002) Network motifs: Simple building blocks of complex networks. Science, 298, 824-827.
19. Palla,G. et al. (2005) Uncovering the overlapping community structure of complex networks in nature and society. Nature, 435, 814.
20. Pržulj,N. (2007) Biological network comparison using graphlet degree distribution. Bioinformatics, 23, e177-e183.
21. Pržulj,N. et al. (2004). Modeling interactome: Scale-free or geometric. Bioinformatics, 20, 3508-3515.
22. Pržulj,N. et al. (2006) Efficient estimation of graphlet frequency distributions in protein-protein interaction networks. Bioinformatics, 22, 974-980.
23. Rives,A.W. and Galitski,T. (2003) Modular organization of cellular networks. PNAS, 100, 1128-1133.
24. Salwinski,L. et al. (2004) The database of interacting proteins: 2004 update. Nucleic Acids Res., 32, 449-451.
25. Sharan,R. et al. (2007) Network-based prediction of protein function. Mol. Syst. Biol., 3, 88.
26. Spirin,V. and Mirny,L.A. (2003) Protein complexes and functional modules in molecular networks. PNAS, 100, 12123-12128.
27. Strogatz,S. (2001) Exploring complex networks. Nature, 410, 268-276.
28. Tong,A. et al. (2001) A combined experimental and computational strategy to define protein interaction networks for peptide recognition modules. Sciencexpress, 10.
29. Wernicke,S. (2006) Efficient detection of network motifs. IEEE/ACM Trans. Comput. Biol., 3, 347-359.
30. Wuchty,S. and Almaas,E. (2005) Peeling the yeast protein network. Proteomics, 5, 444-449.
31. Wuchty,S. et al. (2003) Evolutionary conservation of motif constituents in the yeast protein interactino network. Nat. Genet. 35, 176-179.
32. Yeger-Lotem,E. et al. (2004) Network motifs in integrated cellular networks of transcription-regulation and protein-protein interaction. PNAS, 101, 5934-5939.
33. Yook,S. et al. (2004) Functional and topological characterization of protein interaction networks. Proteomics, 4, 928-942.
34. Zhang,L. et al. (2005) Motifs, themes and thematic maps of an integrated saccharomyces cerevisiae interaction network. J. Biol., 4, 6.
35. Ziv,E. et al. (2005) Information-theoretic approach to network modularity. Phys. Rev. E, 71, 046117.