A regulon consists of a transcription factor (TF) and its direct transcriptional targets, which contain common TF binding sites in their cis-regulatory control elements. The iRegulon plugin allows you to identify regulons using motif and track discovery in an existing network or in a set of co-regulated genes.
* ***Motif discovery*** is performed in proximal and distal sequences, across ten vertebrate genomes, using nearly 10 thousand candidate motifs (position weight matrices or PWMs).
* ***Track discovery*** has been added in version 1.2. It allows detecting TFs using gene rankings according to the highest ChIP peak within the regulatory space using more than one thousand ChIP-Seq tracks.
* The output of iRegulon is a list of enriched motifs/tracks, alongside with candidate transcription factors. The ***Motif2TF*** associations are based on PWM annotation, the use of TF homology, and of motif similarity.
* New networks can be automatically generated based on the ***predicted TF-target interactions***.
* The iRegulon plugin can also be used to query a TF-targets database made of ***high-confidence target genes*** predicted from the systematic analysis of thousands of cancer gene signatures.
* Supported organisms are ***human***, ***mouse*** and ***fly***.
*A full version of the plugin including TRANSFAC Professional motifs is provided from the website http://iregulon.aertslab.org/download.html
(To download the TRANSFAC PRO version, the user will need to have a valid subscription to TRANSFAC Professional).*
*Published now in [http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003731 PLOS Computational Biology].*
