Syntons, metabolons and interactons: An exact graph-theoretical approach for exploring neighbourhood between genomic and functional data

Bioinformatics

Volumn 21, Issue 23, 2005, Pages 4209-4215

  Boyer, Frédéric ^a   Morgat, Anne ^b   Labarre, Laurent ^c   Pothier, Joël ^d   Viari, Alain ^a  

^a INRIA RHÔNE ALPES   (France)

^b SWISS INSTITUTE OF BIOINFORMATICS   (Switzerland)

^c Genoscope   (France)

^d SORBONNE UNIVERSITÉ   (France)

Author keywords

[No Author keywords available]

Indexed keywords

CONTIG; MULTIENZYME COMPLEX;

ANALYTIC METHOD; ARTICLE; CONTROLLED STUDY; DATA ANALYSIS; FUNCTIONAL GENOMICS; GENETIC ALGORITHM; INFORMATION PROCESSING; MOLECULAR BIOLOGY; PRIORITY JOURNAL; PROTEIN PROTEIN INTERACTION; THEORETICAL STUDY;

EID: 28444453303     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/bti711     Document Type: Article

References (17)

1. Alm,E. and Arkin,A.P. (2003) Biological networks. Curr. Opin. Struct. Biol., 13, 193-202.
2. Altschul,S.F. et al. (1990) Basic local alignment search tool. J. Mol. Biol., 215, 403-410.
3. Gai,A.-T., Habib,M., Paul,C. and Raffinot,M. (2003) Identifying common connected components of graphs. Report RR-LIRMM-03016. LIRMM, Université de Montpellier 2, France.
4. Galperin,M.Y. and Koonin,E.V. (2000) Who's your neighbor? New computational approaches for functional genomics Nat. Biotechnol., 18, 609-613.
5. Habib,M., Paul,C. and Raffinot,M. (2004) Maximal common connected sets of interval graphs. Proceedings of Combinatorial Pattern Matching: 15th Annual Symposium, CPM 2004, Istanbul, Turkey, July 5-7 2004, LNCS, 3109, pp. 359-372.
6. Kanehisa,M. et al. (2004) The KEGG resource for deciphering the genome. Nucleic Acids Res., 32, D277-D280.
7. Kelley,B.P. et al. (2003) Conserved pathways within bacteria and yeast as revealed by global protein network alignment Proc. Natl Acad. Sci. USA, 100, 11394-11399.
8. Marcotte,E.M. et al. (1999) Detecting protein function and protein-protein interactions from genome sequences. Science, 285, 751-753.
9. Ogata,H. et al. (2000) A heuristic graph comparison algorithm and its application to detect functionally related enzyme clusters. Nucleic Acids Res., 28, 4021-4028.
10. Overbeek,R. et al. (1999) The use of gene clusters to infer functional coupling. Proc. Natl Acad. Sci. USA, 96, 2896-2901.
11. Salgado,H. et al. (2004) RegulonDB (version 4.0): Transcriptional regulation, operon organization and growth conditions in Escherichia coli K-12. Nucleic Acids Res., 32, D303-D306.
12. Salwinski,L. et al. (2004) The database of interacting proteins: 2004 update. Nucleic Acids Res., 32, D449-D451.
13. Sharan,R. et al. (2005) Conserved patterns of protein interaction in multiple species. Proc. Natl Acad. Sci. USA, 102, 1974-1979.
14. Snel,B. et al. (2002) The identification of functional modules from the genomic association of genes. Proc. Natl Acad. Sci. USA, 99, 5890-5895.
15. Tatusov,R.L. et al. (1997) A genomic perspective on protein families. Science, 278, 631-637.
16. Yanai,I. and DeLisi,C. (2002) The society of genes: Networks of functional links between genes from comparative genomics. Genome Biol., 3, research0064.
17. Zheng,Y. et al. (2002) Computational identification of operons in microbial genomes. Genome Res., 12, 1221-1230.