New methods for joint analysis of biological networks and expression data

Bioinformatics

Volumn 20, Issue 10, 2004, Pages 1517-1521

  Sohler, Florian ^a   Hanisch, Daniel ^b   Zimmer, Ralf ^a  

^a UNIVERSITY OF MUNICH   (Germany)

^b Schloss Birlinghoven   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

MITOGEN ACTIVATED PROTEIN KINASE; TRANSCRIPTION FACTOR;

ALGORITHM; ANALYTIC METHOD; ARTICLE; COMPUTER ANALYSIS; COMPUTER INTERFACE; COMPUTER NETWORK; COMPUTER PROGRAM; CONTROLLED STUDY; DATA ANALYSIS; EMBEDDING; EXPERIMENTAL DESIGN; GENE EXPRESSION; GENETIC REGULATION; HYPOTHESIS; NONHUMAN; PRIORITY JOURNAL; SACCHAROMYCES CEREVISIAE; SIGNAL TRANSDUCTION; VALIDATION PROCESS;

EID: 3142706495     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/bth112     Document Type: Article

References (20)

1. Bardwell,L., Cook,J., Chang,E., Cairns,B. and Thorner,J. (1996) Signaling in the yeast pheromone response pathway: specific and high-affinity interaction of the mitogen-activated protein (MAP) kinases Kss1 and Fus3 with the upstream MAP kinase kinase Ste7. Mol. Cell Biol., 16, 3637-3650.
2. Daignan-Fornier,B. and Fink,G. (1992) Coregulation of purine and histidine biosynthesis by the transcriptional activators BAS1 and BAS2. Proc. Natl Acad. Sci., USA, 89, 6746-6750.
3. Fisher,R. (1932) Statistical Methods for Research Workers, 4th edn. Oliver and Boyd, London.
4. Guetsova,M.L., Lecoq,K. and Daignan-Fornier,B. (1997) The isolation and characterization of Saccharomyces cerevisiae mutants that constitutively express purine biosynthetic genes. Genetics, 147, 383-397.
5. Hanisch,D., Fluck,J., Mevissen,H.T. and Zimmer,R. (2003) Playing biology's name game: identifying protein names in scientific text. Pac. Symp. Biocomput., 403-414.
6. Hanisch,D., Zien,A., Zimmer,R. and Lengauer,T. (2002) Co-clustering of biological networks and gene expression data. Bioinformatics, 18 (Suppl. 1), S145-S154.
7. Hughes,T.R., Marton,M.J., Jones,A.R., Roberts,C.J., Stoughton,R., Armour,C.D., Bennett,H.A., Coffey,E., Dai,H., He,Y.D. et al. (2000) Functional discovery via a compendium of expression profiles. Cell, 102, 109-126.
8. Ideker,T., Ozier,O., Schwikowski,B. and Siegel,A.F. (2002) Discovering regulatory and signalling circuits in molecular interaction networks. Bioinformatics, 18 (Suppl. 1), S233-S240.
9. Kirkman-Correia,C., Stroke,I. and Fields,S. (1993) Functional domains of the yeast Ste12 protein, a pheromone-responsive transcriptional activator. Mol. Cell. Biol., 13, 3765-3772.
10. Lee,T., Rinaldi,N., Robert,F., Odom,D., Bar-Joseph,Z., Gerber,G., Hannett,N., Harbison,C., Thompson,C., Simon,I. et al. (2002) Transcriptional regulatory networks in Saccharomyces cerevisiae. Science, 298, 799-804.
11. Mewes,H.W., Frishman,D., Guldener,U., Mannhaupt,G., Mayer,K., Mokrejs,M., Morgenstern,B., Munsterkotter,M., Rudd,S. and Weil,B. (2002) MIPS: a database for genomes and protein sequences. Nucleic Acids Res., 30, 31-34.
12. NIH (2000) Pubmed-national library of medicine.
13. Robinson,M.D., Grigull,J., Mohammad,N. and Hughes,T.R. (2002) Funspec: a web-based cluster interpreter for yeast. BMC Bioinformatics, 3, 35.
14. Rolfes,R.J. and Hinnebusch,A.G. (1993) Translation of the yeast transcriptional activator GCN4 is stimulated by purine limitation: implications for activation of the protein kinase GCN2. Mol. Cell Biol., 13, 5099-5111.
15. Tedford,K., Kim,S., Sa,D., Stevens,K. and Tyers,M. (1997) Regulation of the mating pheromone and invasive growth responses in yeast by two MAP kinase substrates. Curr. Biol., 7, 228-238.
16. The Gene Ontology Consortium (2001) Creating the gene ontology resource: design and implementation. Genome Res., 11, 1425.
17. Xenarios,I., Rice,D.W., Salwinski,L., Baron,M.K., Marcotte,E.M. and Eisenberg,D. (2000) DIP: the database of interacting proteins. Nucleic Acids Res., 28, 289-291.
18. Yeang,C.-H. and Jaakola,T. (2003) Physical network models and multi-source data integration. The Seventh Annual International Conference on Research in Computational Molecular Biology (RECOMB 2003). Berlin, April 10-13, ACM Press, NY, USA.
19. Zeitlinger,J., Simon,I., Harbison,C., Hannett,N., Fink,T.V.G. and Young,R. (2003) Program-specific distribution of a transcription factor dependent on partner transcription factor and MAPK signaling. Cell, 113, 395-404.
20. Zien,A., Küffner,R., Zimmer,R. and Lengauer,T. (2000) Analysis of gene expression data with pathway scores. In Altman,R. et al. (eds), Proceedings of the 8th International Conference on Intelligent Systems for Molecular Biology. AAAI, La Jolla, CA, pp. 407-417.