Refined phylogenetic profiles method for predicting protein-protein interactions

Bioinformatics

Volumn 21, Issue 16, 2005, Pages 3409-3415

  Sun, Jingchun ^a   Xu, Jinlin ^a   Liu, Zhen ^b   Zhao, Aimin ^d   Shi, Tieliu ^c   Li, Yixue ^c  

^a SHANGHAI JIAO TONG UNIVERSITY   (China)

^b HUNAN NORMAL UNIVERSITY   (China)

^c Shanghai Jiao Tong University Affiliated Sixth People s Hospital   (China)

^d China National Center for Biotechnology Development   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ALGORITHM; ARTICLE; COMPUTER ANALYSIS; COMPUTER MODEL; CONTROLLED STUDY; GENOME; NONHUMAN; PHYLOGENY; PREDICTION; PRIORITY JOURNAL; PROTEIN FUNCTION; PROTEIN PROTEIN INTERACTION; PROTEOMICS; SEQUENCE HOMOLOGY;

EID: 24044546509     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/bti532     Document Type: Article

References (25)

1. Altschul,S. et al. (1997) Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids. Res. 25, 3389-3402.
2. Auerbach,D. et al. (2002) The post-genomic era of interactive proteomics: Facts and perspectives. Proteomics, 2, 611-623.
3. Chen,Y. and Xu,D. (2003) Computational analyses of high-throughput protein-protein interaction data. Curr. Protein Pept. Sci., 4 159-181.
4. Date,S.V. and Marcotte,E.M. (2003) Discovery of uncharacterized cellular systems by genome-wide analysis of functional linkages. Nat. Biotechnol., 21, 1055-1062.
5. Eisenberg,D. et al. (2000) Protein function in the post-genomic era. Nature, 405, 823-826.
6. Enault,F. et al. (2003) Annotation of bacterial genomes using improved phylogenomic profiles. Bioinformatics, 19(Suppl. 1), i105-i107.
7. Enright,A. et al. (1999) Protein interaction maps for complete genomes based on gene fusion events. Nature, 402, 86-90.
8. Fields,S. and Song,O. (1989) A novel genetic system to detect protein-protein interactions. Nature, 340, 245-246.
9. Gaasterland,T. and Ragan,M.A. (1998) Microbial genescapes: Phyletic and functional patterns of ORF distribution among prokaryotes. Microb. Comp. Genomics, 3, 199-217.
10. Kanehisa,M. et al. (2004) The KEGG resource for deciphering the genome. Nucleic Acids. Res., 32(Database issue), D277-D280.
11. Keseler,I.M. et al. (2005) EcoCyc: A comprehensive database resource for Escherichia coli. Nucleic Acids Res., 33 Database issue), D334-D337.
12. Marcotte,E.M. et al. (1999a) Detecting protein function and protein-protein interactions from genome sequences. Science, 285, 751-753.
13. Marcotte,E.M. et al. (1999b) A combined algorithm for genome-wide prediction of protein function. Nature, 402, 83-86.
14. Marcotte,E.M. et al. (2000) Localizing proteins in the cell from their phylogenetic profiles. Proc. Natl Acad. Sci. USA, 97, 12115-12120.
15. Oliver,S. (2000) Guilt-by-association goes global. Nature, 403 601-603.
16. Overbeek,R. et al. (1999) The use of gene clusters to infer functional coupling. Proc. Natl Acad. Sci. USA, 96, 2896-2901.
17. Pellegrini,M. et al. (1999) Assigning protein functions by comparative genome analysis: Protein phylogenetic profiles. Proc. Natl Acad. Sci. USA, 96, 4285-4288.
18. Salwinski,L. et al. (2004) The Database of Interacting Proteins: 2004 update. Nucleic Acids Res., 32(Database issue), D449-D451.
19. Schwikowski,B. et al. (2000) A network of protein-protein interactions in yeast. Nat. Biotechnol., 18, 1257-1261.
20. Strong,M. et al. (2003) Inference of protein function and protein linkages in Mycobacterium tuberculosis based on prokaryotic genome organization: A combined computational approach. Genome Biol., 4, R59.
21. von Mering,C. et al. (2002) Comparative assessment of large-scale datasets of protein-protein interactions. Nature, 417, 399-403.
22. von Mering,C. et al. (2005) STRING: Known and predicted protein-protein associations, integrated and transferred across organisms. Nucleic Acids Res., 33(Database issue), D433-D437.
23. Walhout,A.J. and Vidal,M. (2001) Protein interaction maps for model organisms. Nat. Rev. Mol. Cell Biol., 2, 55-62.
24. Wu,J. et al. (2003) Identification of functional links between genes using phylogenetic profiles. Bioinformatics, 19, 1524-1530.
25. Zheng,Y. et al. (2002) Genomic functional annotation using co-evolution profiles of gene clusters. Genome Biol., 3, RESEARCH0060.