Discovering regulatory and signalling circuits in molecular interaction networks

Bioinformatics

Volumn 18, Issue SUPPL. 1, 2002, Pages

  Ideker, Trey ^a   Ozier, Owen ^a   Schwikowski, Benno ^b   Siegel, Andrew F ^b,c  

^a WHITEHEAD INSTITUTE FOR BIOMEDICAL RESEARCH   (United States)

^b INSTITUTE FOR SYSTEMS BIOLOGY   (United States)

^c UNIVERSITY OF WASHINGTON   (United States)

Author keywords

Data integration; Gene expression; Molecular interactions; Monte Carlo methods; Simulated annealing

Indexed keywords

ALGORITHM; BIOLOGICAL MODEL; COMPUTER SIMULATION; CONFERENCE PAPER; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETIC DATABASE; GENOMICS; MOLECULAR INTERACTION; PRIORITY JOURNAL; PROTEIN DNA INTERACTION; PROTEIN PROTEIN INTERACTION; PROTEOMICS; SIGNAL TRANSDUCTION; SIMULATION; ARTICLE; EVALUATION; GENETICS; METABOLISM; METHODOLOGY; PHYSIOLOGY; YEAST;

PROTEOME;

ALGORITHMS; COMPUTER SIMULATION; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; MODELS, BIOLOGICAL; PROTEOME; SIGNAL TRANSDUCTION; YEASTS;

EID: 0000801240     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/18.suppl_1.S233     Document Type: Conference Paper

References (18)

1. Altman, R.B. and Raychaudhuri, S. (2001) Whole-genome expression analysis:challenges beyond clustering. Curr. Opin. Struct. Biol., 11, 340-347.
2. Bader, G.D., Donaldson, I., Wolting, C., Ouellette, B.F., Pawson, T. and Hogue, C.W. (2001) BIND-The Biomolecular Interaction Network Database. Nucleic Acids Res., 29, 242-245.
3. Eisen, M.B., Spellman, P.T., Brown, P.O. and Botstein, D. (1998) Cluster analysis and display of genome-wide expression patterns. Proc. Natl Acad. Sci. USA, 95, 14863-14868.
4. Gavin, A.-C., Bosche, M., Krause, R., Grandi, P., and Marzioch, M. (2002) Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature, 415, 141-147.
5. Ideker, I., Thorsson, V., Ranish, J.A., Christmas, R., Buhler, J., Bumgarner, R., Aebersold, R. and Hood, L. (2001) Integrated genomic and proteomic analysis of a systematically perturbed metabolic network. Science, 292, 929-934.
6. Ideker, T., Thorsson, V., Siegel, A. and Hood, L. (2000) Testing for differentially-expressed genes by maximum likelihood analysis of microarray data. J. Comput. Biol., 7, 805-817.
7. Kendall, S.M., Stuart, A. and Ord, J.K. (1987) Kendall's Advanced Theory of Statistics, 5th edition, Oxford University Press, NY, pp. 446.
8. Kerr, M.K. and Churchill, G.A. (2001) Bootstrapping cluster analysis: assessing the reliability of conclusions from microarray experiments. Proc. Natl Acad. Sci. USA, 98, 8961-8965.
9. Kirkpatrick, S., Gelatt, C.D. and Vecchi, M.P. (1983) Optimization by Simulated Annealing. Science, 220, 671-680.
10. Lohr, D., Venkov, P. and Zlatanova, J. (1995) Transcriptional regulation in the yeast GAL gene family: a complex genetic network. Faseb Journal, 9, 777-787.
11. Lundy, M. and Mess, A. (1986) Convergence of an Annealing Algorithm. Mathematical Programming, 34, 111-124.
12. Pilpel, Y., Sudarsanam, P. and Church, G.M. (2001) Identifying regulatory networks by combinatorial analysis of promoter elements. Nat. Genet., 29, 153-159.
13. Ren, B., Robert, J., 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.
14. Rocke, D.M. and Durbin, B. (2001) A model for measurement error for gene expression arrays. J. Comput. Biol., 8, 557-569.
15. Tamayo, P., Slonim, D., Mesirov, J., Zhu, Q., Kitareewan, S., Dmitrovsky, E., Lander, E.S. and Golub, T.R. (1999) Interpreting patterns of gene expression with self-organizing maps: Methods and application to hematopoietic differentiation. Proc. Natl Acad. Sci. USA, 96, 2907-2912.
16. 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.
17. Wingender, E., Chen, X., Fricke, E., Geffers, R., Hehl, R., Liebich, I., Krill, M., Matys, V., Michael, H., Ohnhauser, R. et al., (2001) The TRANSFAC system on geneexpression regulation. Nucleic Acids Res., 29, 281-283.
18. Zhu, H., Bilgin, M., Bangham, R., Hall, D., Casamayor, A., Bertone, P., Lan, N., Jansen, R., Bidlingmaier, S., Houfek, T. et al., (2001) Global analysis of protein activities using proteome chips. Science, 293, 2101-2105.