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Transcriptional regulation of protein complexes in yeast.

Simonis N, van Helden J, Cohen GN, Wodak SJ.

Genome Biol. 2004;5(5):R33. Epub 2004 Apr 30.PMID: 15128447 [PubMed - indexed for MEDLINE]Related articlesFree article

Modularity of the transcriptional response of protein complexes in yeast.

Simonis N, Gonze D, Orsi C, van Helden J, Wodak SJ.

J Mol Biol. 2006 Oct 20;363(2):589-610. Epub 2006 Jul 3.PMID: 16973176 [PubMed - indexed for MEDLINE]Related articles

Correlating overrepresented upstream motifs to gene expression: a computational approach to regulatory element discovery in eukaryotes.

Caselle M, Di Cunto F, Provero P.

BMC Bioinformatics. 2002;3:7. Epub 2002 Feb 14.PMID: 11876822 [PubMed - indexed for MEDLINE]Related articlesFree article

Defining transcription modules using large-scale gene expression data.

Ihmels J, Bergmann S, Barkai N.

Bioinformatics. 2004 Sep 1;20(13):1993-2003. Epub 2004 Mar 25.PMID: 15044247 [PubMed - indexed for MEDLINE]Related articlesFree article

Transcriptional profiling of cross pathway control in Neurospora crassa and comparative analysis of the Gcn4 and CPC1 regulons.

Tian C, Kasuga T, Sachs MS, Glass NL.

Eukaryot Cell. 2007 Jun;6(6):1018-29. Epub 2007 Apr 20.PMID: 17449655 [PubMed - indexed for MEDLINE]Related articlesFree article

Bidirectional promoters generate pervasive transcription in yeast.

Xu Z, Wei W, Gagneur J, Perocchi F, Clauder-Münster S, Camblong J, Guffanti E, Stutz F, Huber W, Steinmetz LM.

Nature. 2009 Feb 19;457(7232):1033-7. Epub 2009 Jan 25.PMID: 19169243 [PubMed - indexed for MEDLINE]Related articlesFree article

Inferring condition-specific modulation of transcription factor activity in yeast through regulon-based analysis of genomewide expression.

Boorsma A, Lu XJ, Zakrzewska A, Klis FM, Bussemaker HJ.

PLoS One. 2008 Sep 3;3(9):e3112.PMID: 18769540 [PubMed - indexed for MEDLINE]Related articlesFree article

Comprehensive analysis of combinatorial regulation using the transcriptional regulatory network of yeast.

Balaji S, Babu MM, Iyer LM, Luscombe NM, Aravind L.

J Mol Biol. 2006 Jun 30;360(1):213-27. Epub 2006 May 3.PMID: 16762362 [PubMed - indexed for MEDLINE]Related articles

Combining pattern discovery and discriminant analysis to predict gene co-regulation.

Simonis N, Wodak SJ, Cohen GN, van Helden J.

Bioinformatics. 2004 Oct 12;20(15):2370-9. Epub 2004 Apr 8.PMID: 15073004 [PubMed - indexed for MEDLINE]Related articlesFree article

Selective inhibition of yeast regulons by daunorubicin: a transcriptome-wide analysis.

Rojas M, Casado M, Portugal J, Piña B.

BMC Genomics. 2008 Jul 30;9:358.PMID: 18667070 [PubMed - indexed for MEDLINE]Related articlesFree article

Systems-level evidence of transcriptional co-regulation of yeast protein complexes.

Lee JW, Zemojtel T, Shakhnovich E.

J Comput Biol. 2009 Feb;16(2):331-9.PMID: 19193150 [PubMed - indexed for MEDLINE]Related articles

The budding yeast rRNA and ribosome biosynthesis (RRB) regulon contains over 200 genes.

Wade CH, Umbarger MA, McAlear MA.

Yeast. 2006 Mar;23(4):293-306.PMID: 16544271 [PubMed - indexed for MEDLINE]Related articles

Genome-wide co-occurrence of promoter elements reveals a cis-regulatory cassette of rRNA transcription motifs in Saccharomyces cerevisiae.

Sudarsanam P, Pilpel Y, Church GM.

Genome Res. 2002 Nov;12(11):1723-31.PMID: 12421759 [PubMed - indexed for MEDLINE]Related articlesFree article

The YEASTRACT database: a tool for the analysis of transcription regulatory associations in Saccharomyces cerevisiae.

Teixeira MC, Monteiro P, Jain P, Tenreiro S, Fernandes AR, Mira NP, Alenquer M, Freitas AT, Oliveira AL, Sá-Correia I.

Nucleic Acids Res. 2006 Jan 1;34(Database issue):D446-51.PMID: 16381908 [PubMed - indexed for MEDLINE]Related articlesFree article

Genome wide identification of regulatory motifs in Bacillus subtilis.

Mwangi MM, Siggia ED.

BMC Bioinformatics. 2003 May 16;4:18. Epub 2003 May 16.PMID: 12749771 [PubMed - indexed for MEDLINE]Related articlesFree article

Computational reconstruction of transcriptional regulatory modules of the yeast cell cycle.

Wu WS, Li WH, Chen BS.

BMC Bioinformatics. 2006 Sep 29;7:421.PMID: 17010188 [PubMed - indexed for MEDLINE]Related articlesFree article

Inferring direct regulatory targets from expression and genome location analyses: a comparison of transcription factor deletion and overexpression.

Tang L, Liu X, Clarke ND.

BMC Genomics. 2006 Aug 22;7:215.PMID: 16923194 [PubMed - indexed for MEDLINE]Related articlesFree article

Mining yeast transcriptional regulatory modules from factor DNA-binding sites and gene expression data.

Pham TH, Satou K, Ho TB.

Genome Inform. 2004;15(2):287-95.PMID: 15706514 [PubMed - indexed for MEDLINE]Related articles

Upstream sequence elements direct post-transcriptional regulation of gene expression under stress conditions in yeast.

Lawless C, Pearson RD, Selley JN, Smirnova JB, Grant CM, Ashe MP, Pavitt GD, Hubbard SJ.

BMC Genomics. 2009 Jan 7;10:7.PMID: 19128476 [PubMed - indexed for MEDLINE]Related articlesFree article

Genome-wide analysis of yeast transcription upon calcium shortage.

Lombardía LJ, Becerra M, Rodríguez-Belmonte E, Hauser NC, Cerdán ME.

Cell Calcium. 2002 Aug;32(2):83-91.PMID: 12161108 [PubMed - indexed for MEDLINE]Related articles