Integrating large-scale functional genomic data to dissect the complexity of yeast regulatory networks (original) (raw)
Kulp, D.C. & Jagalur, M. Causal inference of regulator-target pairs by gene mapping of expression phenotypes. BMC Genomics7, 125 (2006). ArticlePubMedPubMed Central Google Scholar
Lum, P.Y. et al. Elucidating the murine brain transcriptional network in a segregating mouse population to identify core functional modules for obesity and diabetes. J. Neurochem.97 (Suppl. 1), 50–62 (2006). ArticleCASPubMed Google Scholar
Mehrabian, M. et al. Integrating genotypic and expression data in a segregating mouse population to identify 5-lipoxygenase as a susceptibility gene for obesity and bone traits. Nat. Genet.37, 1224–1233 (2005). ArticleCASPubMed Google Scholar
Schadt, E.E. et al. An integrative genomics approach to infer causal associations between gene expression and disease. Nat. Genet.37, 710–717 (2005). ArticleCASPubMedPubMed Central Google Scholar
Rual, J.F. et al. Towards a proteome-scale map of the human protein-protein interaction network. Nature437, 1173–1178 (2005). ArticleCASPubMed Google Scholar
Nielsen, J. & Oliver, S. The next wave in metabolome analysis. Trends Biotechnol.23, 544–546 (2005). ArticleCASPubMed Google Scholar
Rajagopalan, D. & Agarwal, P. Inferring pathways from gene lists using a literature-derived network of biological relationships. Bioinformatics21, 788–793 (2005). ArticleCASPubMed Google Scholar
Brem, R.B. & Kruglyak, L. The landscape of genetic complexity across 5,700 gene expression traits in yeast. Proc. Natl. Acad. Sci. USA102, 1572–1577 (2005). ArticleCASPubMed Google Scholar
Brem, R.B., Yvert, G., Clinton, R. & Kruglyak, L. Genetic dissection of transcriptional regulation in budding yeast. Science296, 752–755 (2002). ArticleCASPubMed Google Scholar
MacIsaac, K.D. et al. An improved map of conserved regulatory sites for Saccharomyces cerevisiae. BMC Bioinformatics7, 113 (2006). ArticlePubMedPubMed Central Google Scholar
Lee, T.I. et al. Transcriptional regulatory networks in Saccharomyces cerevisiae. Science298, 799–804 (2002). ArticleCASPubMed Google Scholar
Zhu, J. et al. An integrative genomics approach to the reconstruction of gene networks in segregating populations. Cytogenet. Genome Res.105, 363–374 (2004). ArticleCASPubMed Google Scholar
Zhang, B. & Horvath, S. A general framework for weighted gene co-expression network analysis. Stat. Appl. Genet. Mol. Biol.4, Article17 (2005).
Ghazalpour, A. et al. Integrating genetic and network analysis to characterize genes related to mouse weight. PLoS Genet.2, e130 (2006). ArticlePubMedPubMed Central Google Scholar
Ravasz, E., Somera, A.L., Mongru, D.A., Oltvai, Z.N. & Barabasi, A.L. Hierarchical organization of modularity in metabolic networks. Science297, 1551–1555 (2002). ArticleCASPubMed Google Scholar
Yvert, G. et al. Trans-acting regulatory variation in Saccharomyces cerevisiae and the role of transcription factors. Nat. Genet.35, 57–64 (2003). ArticleCASPubMed Google Scholar
Hughes, T.R. et al. Functional discovery via a compendium of expression profiles. Cell102, 109–126 (2000). ArticleCASPubMed Google Scholar
Deeds, E.J., Ashenberg, O. & Shakhnovich, E.I. A simple physical model for scaling in protein-protein interaction networks. Proc. Natl. Acad. Sci. USA103, 311–316 (2006). ArticleCASPubMed Google Scholar
Palla, G., Derenyi, I., Farkas, I. & Vicsek, T. Uncovering the overlapping community structure of complex networks in nature and society. Nature435, 814–818 (2005). ArticleCASPubMed Google Scholar
Guldener, U. et al. MPact: the MIPS protein interaction resource on yeast. Nucleic Acids Res.34, D436–D441 (2006). ArticlePubMed Google Scholar
Ge, H., Liu, Z., Church, G.M. & Vidal, M. Correlation between transcriptome and interactome mapping data from Saccharomyces cerevisiae. Nat. Genet.29, 482–486 (2001). ArticleCASPubMed Google Scholar
Jansen, R., Greenbaum, D. & Gerstein, M. Relating whole-genome expression data with protein-protein interactions. Genome Res.12, 37–46 (2002). ArticleCASPubMedPubMed Central Google Scholar
Lee, I., Date, S.V., Adai, A.T. & Marcotte, E.M. A probabilistic functional network of yeast genes. Science306, 1555–1558 (2004). ArticleCASPubMed Google Scholar
Lee, S.I., Pe'er, D., Dudley, A.M., Church, G.M. & Koller, D. Identifying regulatory mechanisms using individual variation reveals key role for chromatin modification. Proc. Natl. Acad. Sci. USA103, 14062–14067 (2006). ArticleCASPubMed Google Scholar
Zhu, J. et al. Increasing the power to detect causal associations by combining genotypic and expression data in segregating populations. PLOS Comput. Biol.3, e69 (2007). ArticlePubMedPubMed Central Google Scholar
Tan, K., Shlomi, T., Feizi, H., Ideker, T. & Sharan, R. Transcriptional regulation of protein complexes within and across species. Proc. Natl. Acad. Sci. USA104, 1283–1288 (2007). ArticleCASPubMed Google Scholar
Ogawa, N., DeRisi, J. & Brown, P.O. New components of a system for phosphate accumulation and polyphosphate metabolism in Saccharomyces cerevisiae revealed by genomic expression analysis. Mol. Biol. Cell11, 4309–4321 (2000). ArticleCASPubMedPubMed Central Google Scholar
Ronald, J., Brem, R.B., Whittle, J. & Kruglyak, L. Local regulatory variation in Saccharomyces cerevisiae. PLoS Genet.1, e25 (2005). ArticlePubMedPubMed Central Google Scholar
Giots, F., Donaton, M.C. & Thevelein, J.M. Inorganic phosphate is sensed by specific phosphate carriers and acts in concert with glucose as a nutrient signal for activation of the protein kinase A pathway in the yeast Saccharomyces cerevisiae. Mol. Microbiol.47, 1163–1181 (2003). ArticleCASPubMed Google Scholar
Chen, X.J. Sal1p, a calcium-dependent carrier protein that suppresses an essential cellular function associated with the Aac2 isoform of ADP/ATP translocase in Saccharomyces cerevisiae. Genetics167, 607–617 (2004). ArticleCASPubMedPubMed Central Google Scholar
Deutschbauer, A.M. & Davis, R.W. Quantitative trait loci mapped to single-nucleotide resolution in yeast. Nat. Genet.37, 1333–1340 (2005). ArticleCASPubMed Google Scholar
Sinha, H., Nicholson, B.P., Steinmetz, L.M. & McCusker, J.H. Complex genetic interactions in a quantitative trait locus. PLoS Genet.2, e13 (2006). ArticlePubMedPubMed Central Google Scholar
Pe'er, D., Regev, A., Elidan, G. & Friedman, N. Inferring subnetworks from perturbed expression profiles. Bioinformatics17 (Suppl 1), S215–S224 (2001). ArticlePubMed Google Scholar
Ong, I.M., Glasner, J.D. & Page, D. Modelling regulatory pathways in E. coli from time series expression profiles. Bioinformatics18 (Suppl 1), S241–S248 (2002). ArticlePubMed Google Scholar