PubMed

ModuleFinder and CoReg: alternative tools for linking gene expression modules with promoter sequences motifs to uncover gene regulation mechanisms in plants.

Holt KE, Millar AH, Whelan J.

Plant Methods. 2006 Apr 11;2:8.PMID: 16606469 [PubMed - in process]Related articlesFree article

Genome-wide prediction of transcriptional regulatory elements of human promoters using gene expression and promoter analysis data.

Kim SY, Kim Y.

BMC Bioinformatics. 2006 Jul 4;7:330.PMID: 16817975 [PubMed - indexed for MEDLINE]Related articlesFree article

A cis-regulatory logic simulator.

Zeigler RD, Gertz J, Cohen BA.

BMC Bioinformatics. 2007 Jul 27;8:272.PMID: 17662143 [PubMed - indexed for MEDLINE]Related articlesFree article

XcisClique: analysis of regulatory bicliques.

Pati A, Vasquez-Robinet C, Heath LS, Grene R, Murali TM.

BMC Bioinformatics. 2006 Apr 21;7:218.PMID: 16630346 [PubMed - indexed for MEDLINE]Related articlesFree article

FORCA, a promoter element that responds to crosstalk between defense and light signaling.

Evrard A, Ndatimana T, Eulgem T.

BMC Plant Biol. 2009 Jan 7;9:2.PMID: 19128484 [PubMed - indexed for MEDLINE]Related articlesFree article

Seed storage protein gene promoters contain conserved DNA motifs in Brassicaceae, Fabaceae and Poaceae.

Fauteux F, Strömvik MV.

BMC Plant Biol. 2009 Oct 20;9:126.PMID: 19843335 [PubMed - indexed for MEDLINE]Related articlesFree article

CompMoby: comparative MobyDick for detection of cis-regulatory motifs.

Chaivorapol C, Melton C, Wei G, Yeh RF, Ramalho-Santos M, Blelloch R, Li H.

BMC Bioinformatics. 2008 Oct 27;9:455.PMID: 18950538 [PubMed - indexed for MEDLINE]Related articlesFree article

Unraveling transcriptional control in Arabidopsis using cis-regulatory elements and coexpression networks.

Vandepoele K, Quimbaya M, Casneuf T, De Veylder L, Van de Peer Y.

Plant Physiol. 2009 Jun;150(2):535-46. Epub 2009 Apr 8.PMID: 19357200 [PubMed - indexed for MEDLINE]Related articles

PRECISE: software for prediction of cis-acting regulatory elements.

Trindade LM, van Berloo R, Fiers M, Visser RG.

J Hered. 2005 Sep-Oct;96(5):618-22. Epub 2005 Aug 31.PMID: 16135709 [PubMed - indexed for MEDLINE]Related articlesFree article

Meta-analysis of breast cancer microarray studies in conjunction with conserved cis-elements suggest patterns for coordinate regulation.

Smith DD, Saetrom P, Snøve O Jr, Lundberg C, Rivas GE, Glackin C, Larson GP.

BMC Bioinformatics. 2008 Jan 28;9:63.PMID: 18226260 [PubMed - indexed for MEDLINE]Related articlesFree article

Identification of gene co-regulatory modules and associated cis-elements involved in degenerative heart disease.

Danko CG, Pertsov AM.

BMC Med Genomics. 2009 May 28;2:31.PMID: 19476647 [PubMed]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

In silico discovery of transcription regulatory elements in Plasmodium falciparum.

Young JA, Johnson JR, Benner C, Yan SF, Chen K, Le Roch KG, Zhou Y, Winzeler EA.

BMC Genomics. 2008 Feb 7;9:70.PMID: 18257930 [PubMed - indexed for MEDLINE]Related articlesFree article

Genome-wide analysis of ABA-responsive elements ABRE and CE3 reveals divergent patterns in Arabidopsis and rice.

Gómez-Porras JL, Riaño-Pachón DM, Dreyer I, Mayer JE, Mueller-Roeber B.

BMC Genomics. 2007 Aug 1;8:260.PMID: 17672917 [PubMed - indexed for MEDLINE]Related articlesFree article

Development of a novel data mining tool to find cis-elements in rice gene promoter regions.

Doi K, Hosaka A, Nagata T, Satoh K, Suzuki K, Mauleon R, Mendoza MJ, Bruskiewich R, Kikuchi S.

BMC Plant Biol. 2008 Feb 27;8:20.PMID: 18302796 [PubMed - indexed for MEDLINE]Related articlesFree article

PlantPAN: Plant promoter analysis navigator, for identifying combinatorial cis-regulatory elements with distance constraint in plant gene groups.

Chang WC, Lee TY, Huang HD, Huang HY, Pan RL.

BMC Genomics. 2008 Nov 26;9:561.PMID: 19036138 [PubMed - indexed for MEDLINE]Related articlesFree article

Integration of Arabidopsis thaliana stress-related transcript profiles, promoter structures, and cell-specific expression.

Ma S, Bohnert HJ.

Genome Biol. 2007;8(4):R49.PMID: 17408486 [PubMed - indexed for MEDLINE]Related articlesFree article

The regulatory code for transcriptional response diversity and its relation to genome structural properties in A. thaliana.

Walther D, Brunnemann R, Selbig J.

PLoS Genet. 2007 Feb 9;3(2):e11. Epub 2006 Dec 6.PMID: 17291162 [PubMed - indexed for MEDLINE]Related articlesFree article

Characterization of promoter elements required for expression and induction by sucrose of the Arabidopsis COX5b-1 nuclear gene, encoding the zinc-binding subunit of cytochrome c oxidase.

Comelli RN, Viola IL, Gonzalez DH.

Plant Mol Biol. 2009 Apr;69(6):729-43. Epub 2009 Jan 1.PMID: 19125337 [PubMed - indexed for MEDLINE]Related articles

Motif discovery in promoters of genes co-localized and co-expressed during myeloid cells differentiation.

Coppe A, Ferrari F, Bisognin A, Danieli GA, Ferrari S, Bicciato S, Bortoluzzi S.

Nucleic Acids Res. 2009 Feb;37(2):533-49. Epub 2008 Dec 5.PMID: 19059999 [PubMed - indexed for MEDLINE]Related articlesFree article