Kinase Pathway Database: An integrated protein-kinase and NLP-based protein-interaction resource

Genome Research

Volumn 13, Issue 6 A, 2003, Pages 1231-1243

  Koike, Asako ^a,b   Kobayashi, Yoshiyuki ^a,b   Takagi, Toshihisa ^a  

^a UNIVERSITY OF TOKYO   (Japan)

^b HITACHI LTD   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN KINASE;

ABSTRACT REPORT; AMINO ACID SEQUENCE; ARTICLE; ARTIFICIAL INTELLIGENCE; CODING AND CLASSIFICATION; COMPUTER INTERFACE; GENETIC CONSERVATION; HUMAN; INFORMATION PROCESSING; INTERNET; KINASE PATHWAY DATABASE; NONHUMAN; ORTHOLOGY; PRIORITY JOURNAL; PROTEIN DNA INTERACTION; PROTEIN DOMAIN; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; SEQUENCE DATABASE; SPECIES COMPARISON; SPECIES DISTRIBUTION;

ANIMALS; CAENORHABDITIS ELEGANS; CAENORHABDITIS ELEGANS PROTEINS; DATABASES, GENETIC; DROSOPHILA MELANOGASTER; DROSOPHILA PROTEINS; HUMANS; INTERNET; MICE; NATURAL LANGUAGE PROCESSING; PHOSPHOTRANSFERASES; PROTEIN INTERACTION MAPPING; PROTEIN KINASES; RATS; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS;

EUKARYOTA;

EID: 0038479969     PISSN: 10889051     EISSN: None     Source Type: Journal    
DOI: 10.1101/gr.835903     Document Type: Article

References (33)

1. Adachi, J. and Hasegawa, M. 2000. MOLPHY Version 2.3: Programs for phylogenetics, ver. 2.3. Institute of Statistical Mathematics, Tokyo.
2. 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.
3. Apweiler, R., Attwood, T.K., Bairoch, A., Bateman, A., Birney, E., Biswas, M., Bucher, P., Cerutti, L., Corpet, F., Croning, M.D., et al. 2000. InterPro-An integrated documentation resource for protein families, domains, and functional sites. Bioinformatics 16: 1145-1150.
4. Bairoch, A. and Apweiler, R. 2000. The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000. Nucleic Acids Res. 28: 45-48.
5. Bateman, A., Birney, E., Durbin, R., Eddy, S.R., Howe, K.L., and Sonnhammer, E.L.L. 2000. The Pfam protein families databases. Nucleic Acids Res. 28: 263-266.
6. Blaschke, C. and Valencia, A. 2001. The potential use of SUISEKI as a protein interaction discovery tool. Genome Inform. Ser. Workshop Genome Inform. 12: 123-134.
7. Blaschke, C. and Valencia, A. 2002. The frame-based module of the SUISEKI information extraction system. IEEE Intelligent Systems II 2-8.
8. Friedman, C., Kra, P. Yu, H., Krauthammer, M., and Rzhetsky, A. 2001. GENIES: A natural-language processing system for the extraction of molecular pathways from journal articles. Bioinformatics 17: 74-82.
9. Gotoh, O. 1996. Significant improvement in accuracy of multiple protein sequence alignments by iterative refinement as assessed by reference to structural alignments. J. Mol. Biol. 264: 823-838.
10. Hanks, S.K. and Quinn, A.M. 1991. Protein kinase catalytic domain sequence database, identification of conserved features of primary structure and classification of family members. Methods Enzymol. 200: 38-62.
11. Hegyi, H. and Gerstein, M. 1999. The relationship between protein structure and function: A comprehensive survey with application to the yeast genome. J. Mol. Biol. 288: 147-164.
12. Hunter, T. 2000. Signaling-2000 and beyond. Cell 100: 113-127.
13. Hunter, T. and Plowman, G.D. 1997. The protein kinases of budding yeast: Six score and more. Trends Biochem Sci. 22: 18-22.
14. Jenssen, T.K., Laegreid, A., Komorowski, J., and Hovig, E. 2001. A literature network of human genes for high-throughput analysis of gene expression. Nat Genet. 28: 21-28.
15. Kanehisa, M., Goto, S., Kawashima, S., and Nakaya, A. 2002. The KEGG databases at GenomeNet. Nucleic Acids Res. 30: 42-46.
16. Krauthammer, M., Kra, P., Iossifov, I., Gomez, S.M., Hripcsak, G., Hatzivassiloglou, V., Friedman, C., and Rzhetsky, A. 2002. Of truth and pathways: Chasing bits of information through myriads of articles. Bioinformatics (Suppl.) 17: 249-257.
17. Lo Conte, L., Brenner, S.E., Hubbard, T.J., Chothia, C., and Murzin, A.G. 2002. SCOP database in 2002: Refinements accommodate structural genomics. Nucleic Acids Res. 30: 264-267.
18. Manning, G., Plowman, G.D., Hunter, T., and Sudarsanam, S. 2002. Evolution of protein kinase signaling from yeast to man. Trends Biochem Sci. 27: 514-520.
19. McGarvey, P.B., Huang, H., Barker, W.C., Orcutt, B.C., Garavelli, J.S., Srinivasarao, G.Y., Yeh, L.S., Xiao, C., and Wu, C.H. 2000. PIR: A new resource for bioinformatics. Bioinformatics 16: 290-291.
20. Morrison, D.K., Murakami, M.S., and Cleghon V. 2000. Protein kinases and phosphatases in the Drosophila genome. J. Cell Biol. 150: 57-62.
21. Ono, T., Hishigaki, H., Tanigami, A., and Takagi, T. 2001. Automated extraction of information on protein-protein interactions from the biological literature. Bioinformatics 17: 155-161.
22. Page, R.D. 1996. TreeView: An application to display phylogenetic trees on personal computers. Comput. Appl. Biosci. 12: 357-358.
23. Plowman, G.D., Sudarsanam, S., Bingham, J., Whyte, D., Hunter, T. 1999. The protein kinases of Caenorhabditis elegans: A model for signal transduction in multicellular organisms. Proc. Natl. Acad. Sci. USA 96: 13603-13610.
24. Rindflesch, T.C., Tanabe L., Weinstein J.N., and Hunter L. 2000. EDGAR: Extraction of drugs, genes, and relations from the biomedical literature. Pac. Symp. Biocomput. 517-528.
25. Schacherer, F., Choi, C., Gotze, U., Krull, M., Pistor, S., and Wingender, E. 2001. The TRANSPATH signal transduction database: A knowledge base on signal transduction networks. Bioinformatics 17: 1053-1057.
26. Sekimizu, T., Park, H.S., and Tsujii, J. 1998. Identifying the interaction between genes and gene products based on frequently seen verbs in Medline abstracts. Genome Inform. Ser. Workshop Genome. Inform. 9: 62-71.
27. Smith, C.M. 1997. The protein kinase resource and other bioinformation resources. Prog. Biophys. Mol. Biol. 71: 525-533.
28. Stapley, B.J and Benoit, G. 2000. Biobibliometrics: Information retrieval and visualization from co-occurrences of gene names in Medline abstracts. Pac. Symp. Biocomput. 529-540.
29. Thompson, J.D., Higgins, D.G., and Gibson, T.J. 1994. ClustalW: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22: 4673-4680.
30. Thompson, J.D., Gibson, T.J., Plewniak, F., Jeanmougin, F., and Higgins, D.G. 1997. The CLUSTALwindows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25: 4876-4882.
31. Tusnady, G.E. and Simon, I. 2001. The HMMTOP transmembrane topology prediction server. Bioinformatics 17: 849-850.
32. Xenarios, I., Salwinski, L., Duan, X.J., Higney, P., Kim, S.M., and Eisenberg, D. 2002. DIP, the Database of Interacting Proteins: A research tool for studying cellular networks of protein interactions. Nucleic Acids Res. 30: 303-305.
33. Yasuzawa, Y. and Nomura, K. 1994. Operation Research: Its Technique and Application. pp. 137-54. Corona Publishing Co., Tokyo, Japan.