RT Journal Article
SR Electronic
T1 CAGEd-oPOSSUM: motif enrichment analysis from CAGE-derived TSSs
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 040667
DO 10.1101/040667
A1 David J. Arenillas
A1 Alistair R. R. Forrest
A1 Hideya Kawaji
A1 Timo Lassmann
A1 The FANTOM Consortium
A1 Wyeth W. Wasserman
A1 Anthony Mathelier
YR 2016
UL http://biorxiv.org/content/early/2016/02/22/040667.abstract
AB Summary: With the emergence of large-scale Cap Analysis of Gene Expression data sets from individual labs and the FANTOM consortium, one can now analyze the cis-regulatory regions associated with gene transcription at an unprecedented level of refinement. By coupling transcription factor binding site (TFBS) enrichment analysis with CAGE-derived cis-regulatory regions, CAGEd-oPOSSUM can identify TFs that act as key regulators of genes involved in specific mammalian cell and tissue types. The webtool allows for the analysis of CAGE-derived transcription start sites (TSSs) either (i) provided by the user or (ii) selected from ~1,300 mammalian samples from the FANTOM5 project with pre-computed TFBS predicted with JASPAR TF binding profiles. The tool can help power insights into the transcriptional regulation of genes through the study of the specific usage of TSSs within specific cell types and/or under specific conditions.Availability and implementation: The CAGEd-oPOSUM web tool is implemented in Perl, MySQL, and Apache and is available at http://cagedop.cmmt.ubc.ca/CAGEd_oPOSSUM. The source code is freely available from GitHub at https://github.com/wassermanlab/CAGEd-oPOSSUM.Contact: dave{at}cmmt.ubc.ca, wyeth{at}cmmt.ubc.ca, and anthony.mathelier{at}gmail.com.Supplementary information: Supplementary Figures are available on the journal website. Supplementary Data is available at http://cagedop.cmmt.ubc.ca/CAGEd_oPOSSUM/archived_results/.