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Items: 1 to 20 of 345

1.

Combined analysis of expression data and transcription factor binding sites in the yeast genome.

Nagaraj VH, O'Flanagan RA, Bruning AR, Mathias JR, Vershon AK, Sengupta AM.

BMC Genomics. 2004 Aug 26;5(1):59.

2.

Identification of estrogen-responsive genes using a genome-wide analysis of promoter elements for transcription factor binding sites.

Kamalakaran S, Radhakrishnan SK, Beck WT.

J Biol Chem. 2005 Jun 3;280(22):21491-7. Epub 2005 Mar 24.

3.

FactorY, a bioinformatic resource for genome-wide promoter analysis.

Guruceaga E, Segura V, Corrales FJ, Rubio A.

Comput Biol Med. 2009 Apr;39(4):385-7. doi: 10.1016/j.compbiomed.2009.01.008. Epub 2009 Mar 9.

PMID:
19272592
4.

Combined global localization analysis and transcriptome data identify genes that are directly coregulated by Adr1 and Cat8.

Tachibana C, Yoo JY, Tagne JB, Kacherovsky N, Lee TI, Young ET.

Mol Cell Biol. 2005 Mar;25(6):2138-46.

5.

Genome-scale study of the importance of binding site context for transcription factor binding and gene regulation.

Westholm JO, Xu F, Ronne H, Komorowski J.

BMC Bioinformatics. 2008 Nov 17;9:484. doi: 10.1186/1471-2105-9-484.

6.

Inference of combinatorial regulation in yeast transcriptional networks: a case study of sporulation.

Wang W, Cherry JM, Nochomovitz Y, Jolly E, Botstein D, Li H.

Proc Natl Acad Sci U S A. 2005 Feb 8;102(6):1998-2003. Epub 2005 Jan 31.

7.

Prediction of transcription factor binding sites using genetical genomics methods.

von Rohr P, Friberg MT, Kadarmideen HN.

J Bioinform Comput Biol. 2007 Jun;5(3):773-93.

PMID:
17688316
8.

Genome-wide analysis of gene expression regulated by the calcineurin/Crz1p signaling pathway in Saccharomyces cerevisiae.

Yoshimoto H, Saltsman K, Gasch AP, Li HX, Ogawa N, Botstein D, Brown PO, Cyert MS.

J Biol Chem. 2002 Aug 23;277(34):31079-88. Epub 2002 Jun 10.

9.

Transcriptional regulatory networks and the yeast cell cycle.

Futcher B.

Curr Opin Cell Biol. 2002 Dec;14(6):676-83. Review.

PMID:
12473339
10.

CORE_TF: a user-friendly interface to identify evolutionary conserved transcription factor binding sites in sets of co-regulated genes.

Hestand MS, van Galen M, Villerius MP, van Ommen GJ, den Dunnen JT, 't Hoen PA.

BMC Bioinformatics. 2008 Nov 26;9:495. doi: 10.1186/1471-2105-9-495.

11.

Genome-wide allele- and strand-specific expression profiling.

Gagneur J, Sinha H, Perocchi F, Bourgon R, Huber W, Steinmetz LM.

Mol Syst Biol. 2009;5:274. doi: 10.1038/msb.2009.31. Epub 2009 Jun 16.

12.
13.

Seed-based systematic discovery of specific transcription factor target genes.

Mrowka R, Blüthgen N, Fähling M.

FEBS J. 2008 Jun;275(12):3178-92. doi: 10.1111/j.1742-4658.2008.06471.x. Epub 2008 May 13.

14.
15.

Identifying transcription factor targets using enhanced Bayesian classifier.

He D, Zhou D, Zhou Y.

Comput Biol Chem. 2007 Oct;31(5-6):355-60. Epub 2007 Aug 19.

PMID:
17890157
16.
17.

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

Segal E, Shapira M, Regev A, Pe'er D, Botstein D, Koller D, Friedman N.

Nat Genet. 2003 Jun;34(2):166-76.

PMID:
12740579
18.

Target gene identification from expression array data by promoter analysis.

Werner T.

Biomol Eng. 2001 Mar;17(3):87-94. Review.

PMID:
11222983
19.

Clustering and re-clustering for pattern discovery in gene expression data.

Ma PC, Chan KC, Chiu DK.

J Bioinform Comput Biol. 2005 Apr;3(2):281-301.

PMID:
15852506
20.

Promoter analysis of co-regulated genes in the yeast genome.

Zhang MQ.

Comput Chem. 1999 Jun 15;23(3-4):233-50.

PMID:
10404618

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