TFM-Explorer

What is TFM-Explorer?

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

scans sequences for detecting all potential transcription factor binding sites, using weight matrices from JASPAR or TRANSFAC (disclaimer)
extracts significant clusters (region of the input sequences associated with a factor) by calculated a score function

TFM-Explorer allows also to visualize the result clusters and their putative transcription factor biding 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 Acid 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