iRegulon

Detects master regulators and cis-regulatory interactions
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].*

1.3

Works with Cytoscape 3.2

Release Notes

The selected transcription factor for each motif cluster in transcription factor view is now chosen deterministically.

1.2

Works with Cytoscape 3.1

Release Notes

This version includes track discovery and a large motif collection with nearly 10K PWMs. Cytoscape 3.1.x plugin: <ul> <li>bug fixes and adaptation to cytoscape 3.</li> <li>new iregulon visual style.</li> <li>edge color matching cluster color.</li> </ul>

CYTOSCAPE 3

Version 1.3

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Released 13 Feb 2015

Works with Cytoscape 3.2

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CYTOSCAPE 2

Version 1.3

Released 12 Feb 2015

Works with Cytoscape 2.8

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