TFM-Explorer: mining cis-regulatory regions in genomes
Open Access
- 3 June 2010
- journal article
- research article
- Published by Oxford University Press (OUP) in Nucleic Acids Research
- Vol. 38 (Web erver), W286-W292
- https://doi.org/10.1093/nar/gkq473
Abstract
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.Keywords
This publication has 19 references indexed in Scilit:
- Pscan: finding over-represented transcription factor binding site motifs in sequences from co-regulated or co-expressed genesNucleic Acids Research, 2009
- PASTAA: identifying transcription factors associated with sets of co-regulated genesBioinformatics, 2008
- Analysis of Porcine Transcriptional Response to Salmonella enterica serovar Choleraesuis suggests novel targets of NFkappaB are activated in the Mesenteric Lymph NodeBMC Genomics, 2008
- TiGER: A database for tissue-specific gene expression and regulationBMC Bioinformatics, 2008
- Assessment of composite motif discovery methodsBMC Bioinformatics, 2008
- Efficient and accurate P-value computation for Position Weight MatricesAlgorithms for Molecular Biology, 2007
- JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 updateNucleic Acids Research, 2007
- oPOSSUM: integrated tools for analysis of regulatory motif over-representationNucleic Acids Research, 2007
- NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteinsNucleic Acids Research, 2007
- WebLogo: A Sequence Logo Generator: Figure 1Genome Research, 2004