PathBLAST: A tool for alignment of protein interaction networks

Nucleic Acids Research

Volumn 32, Issue WEB SERVER ISS., 2004, Pages

  Kelley, Brian P ^c   Yuan, Bingbing ^c   Lewitter, Fran ^c   Sharan, Roded ^a   Stockwell, Brent R ^c   Ideker, Trey ^b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c WHITEHEAD INSTITUTE FOR BIOMEDICAL RESEARCH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID SEQUENCE; ARTICLE; CAENORHABDITIS ELEGANS; COMPARATIVE GENE MAPPING; COMPUTER PROGRAM; CONSERVATION BIOLOGY; DATA BASE; DROSOPHILA MELANOGASTER; HELICOBACTER PYLORI; INTERNET; MOLECULAR EVOLUTION; ORTHOLOGY; PRIORITY JOURNAL; PROTEIN INTERACTION; PROTEIN METABOLISM; PROTEIN PROTEIN INTERACTION; PROTEIN TARGETING; SACCHAROMYCES CEREVISIAE; SEQUENCE ALIGNMENT; SPECIES DIFFERENCE;

ANIMALS; INTERNET; PROTEIN INTERACTION MAPPING; SEQUENCE ANALYSIS, PROTEIN; SIGNAL TRANSDUCTION; SOFTWARE; USER-COMPUTER INTERFACE;

CAENORHABDITIS; CAENORHABDITIS ELEGANS; DROSOPHILA MELANOGASTER; HELICOBACTER; HELICOBACTER PYLORI; MELANOGASTER; SACCHAROMYCES; SACCHAROMYCES CEREVISIAE;

EID: 3442886313     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkh411     Document Type: Article

References (24)

1. Fields,S. and Song,O. (1989) A novel genetic system to detect protein-protein interactions. Nature, 340, 245-246.
2. Aebersold,R. and Mann,M. (2003) Mass spectrometry-based proteomics. Nature, 422, 198-207.
3. Iyer,V.R., Horak,C.E., Scafe,C.S., Botstein,D., Snyder,M. and Brown,P.O. (2001) Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF. Nature, 409, 533-538.
4. Ren,B., Robert,F., Wyrick,J.J., Aparicio,O., Jennings,E.G., Simon,I., Zeitlinger,J., Schreiber,J., Hannett,N., Kanin,E. et al. (2000) Genome-wide location and function of DNA binding proteins. Science, 290, 2306-2309.
5. Rain,J.C., Selig,L., De Reuse,H., Battaglia,V., Reverdy,C., Simon,S., Lenzen,G., Petel,F., Wojcik,J., Schachter,V. et al. (2001) The protein-protein interaction map of Helicobacter pylori. Nature, 409, 211-215.
6. Uetz,P., Giot,L., Cagney,G., Mansfield,T.A., Judson,R.S., Knight,J.R., Lockshon,D., Narayan,V., Srinivasan,M., Pochart,P. et al. (2000) A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature, 403, 623-627.
7. Ito,T., Chiba,T., Ozawa,R., Yoshida,M., Hattori,M. and Sakaki,Y. (2001) A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc. Natl Acad. Sci. USA, 98, 4569-4574.
8. Lee,T.I., Rinaldi,N.J., Robert,F., Odom,D.T., Bar-Joseph,Z., Gerber,G.K., Hannett,N.M., Harbison,C.T., Thompson,C.M., Simon,I. et al. (2002) Transcriptional regulatory networks in Saccharomyces cerevisiae. Science, 298, 799-804.
9. Ho,Y., Gruhler,A., Heilbut,A., Bader,G.D., Moore,L., Adams,S.L., Millar,A., Taylor,P., Bennett,K., Boutilier,K. et al. (2002) Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature, 415, 180-183.
10. Gavin,A.C., Bosche,M., Krause,R., Grandi,P., Marzioch,M., Bauer,A., Schultz,J., Rick,J.M., Michon,A.M., Cruciat,C.M. et al. (2002) Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature, 415, 141-147.
11. Li,S., Armstrong,C.M., Bertin,N., Ge,H., Milstein,S., Boxem,M., Vidalain,P.O., Han,J.D., Chesneau,A., Hao,T. et al. (2004) A map of the interactome network of the metazoan C. elegans. Science, 303, 540-543.
12. Giot,L., Bader,J.S., Brouwer,C., Chaudhuri,A., Kuang,B., Li,Y., Hao,Y.L., Ooi,C.E., Godwin,B., Vitols,E. et al. (2003) A protein interaction map of Drosophila melanogaster. Science, 302, 1727-1736.
13. von Mering,C., Krause,R., Snel,B., Cornell,M., Oliver,S.G., Fields,S. and Bork,P. (2002) Comparative assessment of large-scale data sets of protein-protein interactions. Nature, 417, 399-403.
14. Ideker,T. and Lauffenburger,D.A. (2003) Building with a scaffold: emerging strategies for high- to low-level cellular modeling. Trends Biotechnol., 21, 255-262.
15. Forst,C.V. and Schulten,K. (1999) Evolution of metabolisms: a new method for the comparison of metabolic pathways using genomics information. J. Comput. Biol., 6, 343-360.
16. Ogata,H., Fujibuchi,W., Goto,S. and Kanehisa,M. (2000) A heuristic graph comparison algorithm and its application to detect functionally related enzyme clusters. Nucleic Acids Res., 28, 4021-4028.
17. Dandekar,T., Schuster,S., Snel,B., Huynen,M. and Bork,P. (1999) Pathway alignment: application to the comparative analysis of glycolytic enzymes. Biochem. J., 343, 115-124.
18. Kelley,B.P., Sharan,R., Karp,R.M., Sittler,T., Root,D.E., Stockwell,B.R. and Ideker,T. (2003) Conserved pathways within bacteria and yeast as revealed by global protein network alignment. Proc. Natl Acad. Sci., USA, 100, 11394-11399.
19. Altschul,S.F., Madden,T.L., Schaffer,A.A., Zhang,J., Zhang,Z., Miller,W. and Lipman,D.J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res., 25, 3389-3402.
20. Sharan,R., Ideker,T., Kelley,B.P., Shamir,R. and Karp,R. (2004) Identification of protein complexes by comparative analysis of yeast and bacterial protein interaction data. Proceedings of the Eighth Annual International Conference on Research in Computational Molecular Biology - RECOMB, San Diego, CA, pp. 282-289.
21. Salwinski,L., Miller,C.S., Smith,A.J., Pettit,F.K., Bowie,J.U. and Eisenberg,D. (2004) The Database of Interacting Proteins: 2004 update. Nucleic Acids Res., 32, D449-D451.
22. Christie,K.R., Weng,S., Balakrishnan,R., Costanzo,M.C., Dolinski,K., Dwight,S.S., Engel,S.R., Feierbach,B., Fisk,D.G., Hirschman,J.E. et al. (2004) Saccharomyces Genome Database (SGD) provides tools to identify and analyze sequences from Saccharomyces cerevisiae and related sequences from other organisms. Nucleic Acids Res., 32, D311-D314.
23. Salgado,H., Gama-Castro,S., Martinez-Antonio,A., Diaz-Peredo,E., Sanchez-Solano,F., Peralta-Gil,M., Garcia-Alonso,D., Jimenez-Jacinto,V., Santos-Zavaleta,A., Bonavides-Martinez,C. 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.
24. Shannon,P., Markiel,A., Ozier,O., Baliga,N.S., Wang,J.T., Ramage,D., Amin,N., Schwikowski,B. and Ideker,T. (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res., 13, 2498-2504.