TFM-Explorer

What is TFM-Explorer?

TFM-Explorer (Transcription Factor Matrix Explorer) is a program for analysing regulatory regions in eukaryotic genomes.
It takes a set of coregulated gene sequences, and searches for locally overrepresented transcription factor binding sites.
The algorithm proceeds in two steps:

The method takes advantage of spatial conservation in the sequences and supports multiple species. TFM-Explorer allows also to visualize the result clusters and their putative transcription factor binding sites on the input sequences, and to search for cis-regulatory modules.

Example

>Human target genes
NM_000040
NM_000043
NM_000073
NM_000074
NM_000118
NM_000201
NM_000367
...
scanned from 2000bp upstream the transcription start site (TSS) until the TSS

visualization

Publications

TFM-Explorer: mining cis-regulatory regions in genomes
Laurie Tonon, Helene Touzet and Jean-Stephane Varre
Nucleic Acids Research 2010 - [abstract]

Predicting transcription factor binding sites using local over-representation and comparative genomics
Matthieu Defrance, Helene Touzet
BMC Bioinformatics 2006 - [abstract]

Availability

You could use TFM-Explorer via the web interface.
You can also download a command line version here.