PubMed

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.PMID: 19014636 [PubMed - indexed for MEDLINE]Related articlesFree article

Integrating genomic data to predict transcription factor binding.

Holloway DT, Kon M, DeLisi C.

Genome Inform. 2005;16(1):83-94.PMID: 16362910 [PubMed - indexed for MEDLINE]Related articles

Defining transcriptional networks through integrative modeling of mRNA expression and transcription factor binding data.

Gao F, Foat BC, Bussemaker HJ.

BMC Bioinformatics. 2004 Mar 18;5:31.PMID: 15113405 [PubMed - indexed for MEDLINE]Related articlesFree article

Position specific variation in the rate of evolution in transcription factor binding sites.

Moses AM, Chiang DY, Kellis M, Lander ES, Eisen MB.

BMC Evol Biol. 2003 Aug 28;3:19. Epub 2003 Aug 28.PMID: 12946282 [PubMed - indexed for MEDLINE]Related articlesFree article

Condition specific transcription factor binding site characterization in Saccharomyces cerevisiae.

Harrison R, DeLisi C.

Bioinformatics. 2002 Oct;18(10):1289-96.PMID: 12376372 [PubMed - indexed for MEDLINE]Related articlesFree article

An HMG protein, Hmo1, associates with promoters of many ribosomal protein genes and throughout the rRNA gene locus in Saccharomyces cerevisiae.

Hall DB, Wade JT, Struhl K.

Mol Cell Biol. 2006 May;26(9):3672-9.PMID: 16612005 [PubMed - indexed for MEDLINE]Related articlesFree article

Expression of the INO2 regulatory gene of Saccharomyces cerevisiae is controlled by positive and negative promoter elements and an upstream open reading frame.

Eiznhamer DA, Ashburner BP, Jackson JC, Gardenour KR, Lopes JM.

Mol Microbiol. 2001 Mar;39(5):1395-405.PMID: 11251853 [PubMed - indexed for MEDLINE]Related articles

Global nucleosome occupancy in yeast.

Bernstein BE, Liu CL, Humphrey EL, Perlstein EO, Schreiber SL.

Genome Biol. 2004;5(9):R62. Epub 2004 Aug 20.PMID: 15345046 [PubMed - indexed for MEDLINE]Related articlesFree article

Identifying promoter features of co-regulated genes with similar network motifs.

Harari O, del Val C, Romero-Zaliz R, Shin D, Huang H, Groisman EA, Zwir I.

BMC Bioinformatics. 2009 Apr 29;10 Suppl 4:S1.PMID: 19426448 [PubMed - indexed for MEDLINE]Related articlesFree article

Cbf1p is required for chromatin remodeling at promoter-proximal CACGTG motifs in yeast.

Kent NA, Eibert SM, Mellor J.

J Biol Chem. 2004 Jun 25;279(26):27116-23. Epub 2004 Apr 24.PMID: 15111622 [PubMed - indexed for MEDLINE]Related articlesFree article

Genome-wide expression profiling, in vivo DNA binding analysis, and probabilistic motif prediction reveal novel Abf1 target genes during fermentation, respiration, and sporulation in yeast.

Schlecht U, Erb I, Demougin P, Robine N, Borde V, Nimwegen E, Nicolas A, Primig M.

Mol Biol Cell. 2008 May;19(5):2193-207. Epub 2008 Feb 27.PMID: 18305101 [PubMed - indexed for MEDLINE]Related articlesFree article

A computational "genome walk" technique to identify regulatory interactions in gene networks.

Wagner A.

Pac Symp Biocomput. 1998:264-78.PMID: 9697188 [PubMed - indexed for MEDLINE]Related articlesFree article

The design of transcription-factor binding sites is affected by combinatorial regulation.

Bilu Y, Barkai N.

Genome Biol. 2005;6(12):R103. Epub 2005 Dec 2.PMID: 16356266 [PubMed - indexed for MEDLINE]Related articlesFree article

Transcriptional activation of human zeta 2 globin promoter by the alpha globin regulatory element (HS-40): functional role of specific nuclear factor-DNA complexes.

Zhang Q, Reddy PM, Yu CY, Bastiani C, Higgs D, Stamatoyannopoulos G, Papayannopoulou T, Shen CK.

Mol Cell Biol. 1993 Apr;13(4):2298-308.PMID: 8455611 [PubMed - indexed for MEDLINE]Related articlesFree article

A rice functional transcriptional activator, RISBZ1, responsible for endosperm-specific expression of storage protein genes through GCN4 motif.

Onodera Y, Suzuki A, Wu CY, Washida H, Takaiwa F.

J Biol Chem. 2001 Apr 27;276(17):14139-52. Epub 2000 Dec 22.PMID: 11133985 [PubMed - indexed for MEDLINE]Related articlesFree article

Histone H2B gene transcription during Xenopus early development requires functional cooperation between proteins bound to the CCAAT and octamer motifs.

Hinkley C, Perry M.

Mol Cell Biol. 1992 Oct;12(10):4400-11.PMID: 1406629 [PubMed - indexed for MEDLINE]Related articlesFree article

Genome-wide analysis of transcriptional dependence and probable target sites for Abf1 and Rap1 in Saccharomyces cerevisiae.

Yarragudi A, Parfrey LW, Morse RH.

Nucleic Acids Res. 2007;35(1):193-202. Epub 2006 Dec 7.PMID: 17158163 [PubMed - indexed for MEDLINE]Related articlesFree article

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.PMID: 15331021 [PubMed - indexed for MEDLINE]Related articlesFree article

Analysis of combinatorial cis-regulation in synthetic and genomic promoters.

Gertz J, Siggia ED, Cohen BA.

Nature. 2009 Jan 8;457(7226):215-8. Epub 2008 Nov 23.PMID: 19029883 [PubMed - indexed for MEDLINE]Related articlesFree article

Regulatory motif finding by logic regression.

Keles S, van der Laan MJ, Vulpe C.

Bioinformatics. 2004 Nov 1;20(16):2799-811. Epub 2004 May 27.PMID: 15166027 [PubMed - indexed for MEDLINE]Related articlesFree article