PubMed

A generic approach to identify Transcription Factor-specific operator motifs; Inferences for LacI-family mediated regulation in Lactobacillus plantarum WCFS1.

Francke C, Kerkhoven R, Wels M, Siezen RJ.

BMC Genomics. 2008 Mar 27;9:145.PMID: 18371204 [PubMed - indexed for MEDLINE]Related articlesFree article

Regulation of arginine biosynthesis in the psychropiezophilic bacterium Moritella profunda: in vivo repressibility and in vitro repressor-operator contact probing.

Xu Y, Sun Y, Huysveld N, Gigot D, Glansdorff N, Charlier D.

J Mol Biol. 2003 Feb 14;326(2):353-69.PMID: 12559906 [PubMed - indexed for MEDLINE]Related articles

Identification and analysis of DNA-binding transcription factors in Bacillus subtilis and other Firmicutes--a genomic approach.

Moreno-Campuzano S, Janga SC, Pérez-Rueda E.

BMC Genomics. 2006 Jun 13;7:147.PMID: 16772031 [PubMed - indexed for MEDLINE]Related articlesFree article

Predicting cis-acting elements of Lactobacillus plantarum by comparative genomics with different taxonomic subgroups.

Wels M, Francke C, Kerkhoven R, Kleerebezem M, Siezen RJ.

Nucleic Acids Res. 2006 Apr 13;34(7):1947-58. Print 2006. Erratum in: Nucleic Acids Res. 2006;34(9):2844. PMID: 16614445 [PubMed - indexed for MEDLINE]Related articlesFree article

Comparative analysis of function and interaction of transcription factors in nematodes: extensive conservation of orthology coupled to rapid sequence evolution.

Haerty W, Artieri C, Khezri N, Singh RS, Gupta BP.

BMC Genomics. 2008 Aug 27;9:399.PMID: 18752680 [PubMed - indexed for MEDLINE]Related articlesFree article

Identification of tissue-specific cis-regulatory modules based on interactions between transcription factors.

Yu X, Lin J, Zack DJ, Qian J.

BMC Bioinformatics. 2007 Nov 9;8:437.PMID: 17996093 [PubMed - indexed for MEDLINE]Related articlesFree article

Thermodynamics of E. coli cytidine repressor interactions with DNA: distinct modes of binding to different operators suggests a role in differential gene regulation.

Tretyachenko-Ladokhina V, Ross JB, Senear DF.

J Mol Biol. 2002 Feb 22;316(3):531-46.PMID: 11866516 [PubMed - indexed for MEDLINE]Related articles

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

Network motif-based identification of transcription factor-target gene relationships by integrating multi-source biological data.

Zhang Y, Xuan J, de los Reyes BG, Clarke R, Ressom HW.

BMC Bioinformatics. 2008 Apr 21;9:203.PMID: 18426580 [PubMed - indexed for MEDLINE]Related articlesFree article

GntR family of regulators in Mycobacterium smegmatis: a sequence and structure based characterization.

Vindal V, Suma K, Ranjan A.

BMC Genomics. 2007 Aug 23;8:289.PMID: 17714599 [PubMed - indexed for MEDLINE]Related articlesFree article

The identification of response regulator-specific binding sites reveals new roles of two-component systems in Bacillus cereus and closely related low-GC Gram-positives.

de Been M, Bart MJ, Abee T, Siezen RJ, Francke C.

Environ Microbiol. 2008 Oct;10(10):2796-809. Epub 2008 Jul 25.PMID: 18662309 [PubMed - indexed for MEDLINE]Related articles

PhyloGibbs: a Gibbs sampling motif finder that incorporates phylogeny.

Siddharthan R, Siggia ED, van Nimwegen E.

PLoS Comput Biol. 2005 Dec;1(7):e67. Epub 2005 Dec 9.PMID: 16477324 [PubMed - indexed for MEDLINE]Related articlesFree article

Meta-analysis discovery of tissue-specific DNA sequence motifs from mammalian gene expression data.

Huber BR, Bulyk ML.

BMC Bioinformatics. 2006 Apr 27;7:229.PMID: 16643658 [PubMed - indexed for MEDLINE]Related articlesFree article

Engineered disulfide linking the hinge regions within lactose repressor dimer increases operator affinity, decreases sequence selectivity, and alters allostery.

Falcon CM, Matthews KS.

Biochemistry. 2001 Dec 25;40(51):15650-9.PMID: 11747440 [PubMed - indexed for MEDLINE]Related articles

Operator DNA sequence variation enhances high affinity binding by hinge helix mutants of lactose repressor protein.

Falcon CM, Matthews KS.

Biochemistry. 2000 Sep 12;39(36):11074-83.PMID: 10998245 [PubMed - indexed for MEDLINE]Related articles

Identification of co-regulated genes through Bayesian clustering of predicted regulatory binding sites.

Qin ZS, McCue LA, Thompson W, Mayerhofer L, Lawrence CE, Liu JS.

Nat Biotechnol. 2003 Apr;21(4):435-9. Epub 2003 Mar 10.PMID: 12627170 [PubMed - indexed for MEDLINE]Related articles

Putative cold acclimation pathways in Arabidopsis thaliana identified by a combined analysis of mRNA co-expression patterns, promoter motifs and transcription factors.

Chawade A, Bräutigam M, Lindlöf A, Olsson O, Olsson B.

BMC Genomics. 2007 Sep 2;8:304.PMID: 17764576 [PubMed - indexed for MEDLINE]Related articlesFree article

Transcriptional regulatory network analysis during epithelial-mesenchymal transformation of retinal pigment epithelium.

Pratt CH, Vadigepalli R, Chakravarthula P, Gonye GE, Philp NJ, Grunwald GB.

Mol Vis. 2008 Aug 4;14:1414-28.PMID: 18682805 [PubMed - indexed for MEDLINE]Related articlesFree article

Alu elements contain many binding sites for transcription factors and may play a role in regulation of developmental processes.

Polak P, Domany E.

BMC Genomics. 2006 Jun 1;7:133.PMID: 16740159 [PubMed - indexed for MEDLINE]Related articlesFree article

Functional consequences of exchanging domains between LacI and PurR are mediated by the intervening linker sequence.

Tungtur S, Egan SM, Swint-Kruse L.

Proteins. 2007 Jul 1;68(1):375-88.PMID: 17436321 [PubMed - indexed for MEDLINE]Related articlesFree article