Module networks: Identifying regulatory modules and their condition-specific regulators from gene expression data

Nature Genetics

Volumn 34, Issue 2, 2003, Pages 166-176

  Segal, Eran ^a   Shapira, Michael ^b   Regev, Aviv ^c,e   Pe'er, Dana ^d   Botstein, David ^b   Koller, Daphne ^a   Friedman, Nir ^d  

^a Stanford University   (United States)

^b STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

^c TEL AVIV UNIVERSITY   (Israel)

^d HEBREW UNIVERSITY OF JERUSALEM   (Israel)

^e HARVARD UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA;

ARTICLE; CELL ACTIVITY; DNA MICROARRAY; GENE CONTROL; GENE EXPRESSION REGULATION; GENE FUNCTION; HYPOTHESIS; NONHUMAN; PRIORITY JOURNAL; SACCHAROMYCES CEREVISIAE;

ALGORITHMS; DATABASES, GENETIC; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, FUNGAL; GENES, FUNGAL; GENES, REGULATOR; MODELS, GENETIC; MODELS, STATISTICAL; MUTATION; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS;

SACCHAROMYCES; SACCHAROMYCES CEREVISIAE;

EID: 0037941585     PISSN: 10614036     EISSN: None     Source Type: Journal    
DOI: 10.1038/ng1165     Document Type: Article

References (46)

1. DeRisi, J.L., Iyer, V.R. & Brown, P.O. Exploring the metabolic and genetic control of gene expression on a genomic scale. Science 278, 680-686 (1997).
2. Spellman, P.T. et al. Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol. Biol. Cell 9, 3273-3297 (1998).
3. Gasch, A.P. et al. Genomic expression programs in the response of yeast cells to environmental changes. Mol. Biol. Cell 11, 4241-4257 (2000).
4. Eisen, M.B., Spellman, P.T., Brown, P.O. & Botstein, D. Cluster analysis and display of genome-wide expression patterns. Proc. Natl. Acad. Sci. USA 95, 14863-14868 (1998).
5. Wu, L.F. et al. Large-scale prediction of Saccharomyces cerevisiae gene function using overlapping transcriptional clusters. Nat. Genet. 31, 255-265 (2002).
6. Ihmels, J. et al. Revealing modular organization in the yeast transcriptional network. Nat. Genet. 31, 370-377 (2002).
7. Halfon, M.S., Grad, Y., Church, G.M. & Michelson, A.M. Computation-based discovery of related transcriptional regulatory modules and motifs using an experimentally validated combinatorial model. Genome Res 12, 1019-1028 (2002).
8. Tanay, A., Sharan, R. & Shamir, R. Discovering statistically significant biclusters in gene expression data. Bioinformatics 18 Suppl 1, S136-S144 (2002).
9. Roth, F.P., Hughes, J.D., Estep, P.W. & Church, G.M. Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantitation. Nat. Biotechnol. 16, 939-945 (1998).
10. Tavazoie, S., Hughes, J.D., Campbell, M.J., Cho, R.J. & Church, G.M. Systematic determination of genetic network architecture. Nat. Genet. 22, 281-285 (1999).
11. Pilpel, Y., Sudarsanam, P. & Church, G.M. Identifying regulatory networks by combinatorial analysis of promoter elements. Nat. Genet. 29, 153-159 (2001).
12. Segal, E., Barash Y., Simon I., Friedman N. & Koller D. From Promoter Sequence to Expression: A Probabilistic Framework. in Proceedings of the 6th International Conference on Research in Computational Molecular Biology (RECOMB) 263-272 (Washington, DC, 2002).
13. Pearl, J. Probabilistic Reasoning in Intelligent Systems (Morgan Kaufmann, Palo Alto, 1988).
14. Dhaseleer, P., Liang, S. & Somogoyi, R. Genetic network inference: from co-expression clustering to reverse engineering. Bioinformatics 16, 707-726 (2000).
15. Pe'er, D., Regev, A., Elidan, G. & Friedman, N. Inferring subnetworks from perturbed expression profiles. Bioinformatics 17 Suppl 1, S215-S224 (2001).
16. Hartemink, A.J., Gifford, D.K., Jaakkola, T.S. & Young, R.A. Combining Location and Expression Data for Principled Discovery of Genetic Regulatory Networks. in Pacific Symposium on Biocomputing (Kauai, 2002).
17. Tanay, A. & Shamir, R. Computational expansion of genetic networks. Bioinformatics 17 Suppl 1, S270-S278 (2001).
18. Pe'er, D., Regev, A. & Tanay, A. Minreg: inferring an active regulator set. Bioinformatics 18 Suppl 1, S258-S267 (2002).
19. Forsburg, S.L. & Guarente, L. Identification and characterization of HAP4: a third component of the CCAAT-bound HAP2/HAP3 heteromer. Genes Dev. 3, 1166-1178 (1989).
20. Norbeck, J. & Blomberg, A. The level of cAMP-dependent protein kinase A activity strongly affects osmotolerance and osmo-instigated gene expression changes in Saccharomyces cerevisiae. Yeast 16, 121-137 (2000).
21. Lenssen, E., Oberholzer, U., Labarre, J., De Virgilio, C. & Collart, M.A. Saccharomyces cerevisiae Ccr4-not complex contributes to the control of Msn2p-dependent transcription by the Ras/cAMP pathway. Mol. Microbiol. 43, 1023-1037 (2002).
22. Winzeler, E.A. et al. Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis. Science 285, 901-906 (1999).
23. Shen-Orr, S.S., Milo, R., Mangan, S. & Alon, U. Network motifs in the transcriptional regulation network of Escherichia coli. Nat. Genet. 31, 64-68 (2002).
24. Lee, T.I. et al Transcriptional regulatory networks in Saccharomyces cerevisiae. Science 298, 799-804 (2002).
25. Milo, R. et al. Network motifs: simple building blocks of complex networks. Science 298, 824-827 (2002).
26. Hlavacek, W.S. & Savageau, M.A. Rules for coupled expression of regulator and effector genes in inducible circuits. J. Mol. Biol. 255, 121-139 (1996).
27. Rosenfeld, N., Elowitz, M.B. & Alon. U. Negative autoregulation speeds the response times of transcription networks. J. Mol. Biol. 323, 785-793 (2002).
28. Roberts, C.J. et al. Signaling and circuitry of multiple MAPK pathways revealed by a matrix of global gene expression profiles. Science 287, 873-880 (2000).
29. Cherry, J.M. et al. SGD: Saccharomyces Genome Database. Nucleic Acids Res. 26, 73-79 (1998).
30. Hodges, P.E., McKee, A.H., Davis, B.P., Payne, W.E. & Garrels, J.I. The Yeast Proteome Database (YPD): a model for the organization and presentation of genomewide functional data. Nucleic Acids Res. 27, 69-73 (1999).
31. Duda, R.O. & Hart, P.E. Pattern classification and scene analysis (John Wiley & Sons, New York, 1973).
32. Ashburner, M. et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet. 25, 25-29 (2000).
33. Mewes, H.W., Albermann, K., Heumann, K., Liebl, S. & Pfeiffer, F. MIPS: a database for protein sequences, homology data and yeast genome information. Nucleic Acids Res. 25, 28-30 (1997).
34. Kanehisa, M., Goto, S., Kawashima, S. & Nakaya, A. The KEGG databases at GenomeNet. Nucleic Acids Res. 30, 42-46 (2002).
35. Segal, E., Taskar, B., Gasch, A., Friedman, N. & Koller, D. Rich probabilistic models for gene expression. Bioinformatics 17 Suppl 1, S243-S252 (2001).
36. Heckerman, D. A tutorial on learning with Bayesian networks. in Learning in Graphical Models (ed. Jordan, M.I.) 301-354 (MIT Press, Cambridge, Massachusetts 1998).
37. Dempster, A.P., Laird, N.M. & Rubin, D.B. Maximum likelihood from incomplete data via the EM algorithm. J. R. Stat. Soc. B39, 1-39 (1977).
38. Friedman, N. The Bayesian structural EM algorithm. in Proceedings of the 14th Conference on Uncertainty in Artificial Intelligence (UAI) 129-138 (1998).
39. Wingender, E. et al. The TRANSFAC system on gene expression regulation. Nucleic Acids Res. 29, 281-283 (2001).
40. Hughes. T.R. et al. Functional discovery via a compendium of expression profiles. Cell 102, 109-126 (2000).
41. Edgar, R., Domrachev, M. & Lash, A.E. Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res. 30, 207-210 (2002).
42. Mayordomo, I., Estruch, F. & Sanz, P. Convergence of the target of rapamycin and the Snf1 protein kinase pathways in the regulation of the subcellular localization of Msn2, a transcriptional activator of STRE (Stress Response Element)-regulated genes. J. Biol. Chem. 277, 35650-35656 (2002).
43. Gorner, W. et al. Nuclear localization of the C2H2 zinc finger protein Msn2p is regulated by stress and protein kinase A activity. Genes Dev. 12, 586-597 (1998).
44. Zahringer, H., Thevelein, J.M. & Nwaka, S. Induction of neutral trehalase Nth1 by heat and osmotic stress is controlled by STRE elements and Msn2/Msn4 transcription factors: variations of PKA effect during stress and growth. Mol. Microbiol. 35, 397-406 (2000).
45. Boy-Marcotte, E., Perrot, M., Bussereau, F., Boucherie, H. & Jacquet, M. Msn2p and Msn4p control a large number of genes induced at the diauxic transition which are repressed by cyclic AMP in Saccharomyces cerevisiae. J. Bacteriol. 180, 1044-1052 (1998)
46. Inoue, Y., Tsujimoto, Y. & Kimura, A. Expression of the glyoxalase I gene of Saccharomyces cerevisiae is regulated by high osmolarity glycerol mitogen-activated protein kinase pathway in osmotic stress response. J Biol. Chem. 273, 2977-2983 (1998).