TFM-Explorer: Mining cis-regulatory regions in genomes

Abstract

DNA-binding transcription factors (TFs) play a central role in transcription regulation, and compu-tational 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 or-ganisms are human, mouse, rat, chicken and dros-ophila. 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. © The Author(s) 2010. Published by Oxford University Press.