TFM-Explorer: mining cis-regulatory regions in genomes.
DNA-binding transcription factors (TFs) play a central role in transcription regulation, and computational approaches that help in elucidating complex mechanisms governing this basic biological process are of great use. In this perspective, we present the TFM-Explorer web server that is a toolbox to identify putative TF binding sites within a set of upstream regulatory sequences of genes sharing some regulatory mechanisms. TFM-Explorer finds local regions showing overrepresentation of binding sites. Accepted organisms are human, mouse, rat, chicken and drosophila. The server employs a number of features to help users to analyze their data: visualization of selected binding sites on genomic sequences, and selection of cis-regulatory modules. TFM-Explorer is available at http://bioinfo.lifl.fr/TFM.
Tonon
Laurie
L
INRIA Lille-Nord Europe, 40 av Halley, 59650 Villeneuve d'Ascq, d'Ascq Cedex, France.
Touzet
Hélène
H
Varré
Jean-Stéphane
JS
D000818:Animals; D001665:Binding Sites; D001921:Brain / Q000378:metabolism; D057225:Data Mining; D023281:Genomics / Q000379:methods; D006801:Humans; D020407:Internet; D051379:Mice; D009132:Muscles / Q000378:metabolism; D051381:Rats; D050436:Regulatory Elements, Transcriptional; D012867:Skin / Q000378:metabolism; D012984:Software; D014157:Transcription Factors / Q000378:metabolism*
D014157:Transcription Factors