CAGEd-oPOSSUM: motif enrichment analysis from CAGE-derived TSSs.
David J Arenillas, Alistair R R Forrest, Hideya Kawaji, Timo Lassmann, FANTOM Consortium, Wyeth W Wasserman, Anthony Mathelier
Author Information
David J Arenillas: Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, BC V5Z 4H4, Canada.
Alistair R R Forrest: Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan RIKEN Omics Science Center, Yokohama, Kanagawa 230-0045 Japan.
Hideya Kawaji: Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan RIKEN Omics Science Center, Yokohama, Kanagawa 230-0045 Japan RIKEN Preventive Medicine and Diagnosis Innovation Program, Wako, Saitama 351-0198, Japan.
Timo Lassmann: Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan RIKEN Omics Science Center, Yokohama, Kanagawa 230-0045 Japan Telethon Kids Institute, The University of Western Australia, Subiaco, WA 6008, Australia.
Wyeth W Wasserman: Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, BC V5Z 4H4, Canada.
Anthony Mathelier: Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, BC V5Z 4H4, Canada Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo and Oslo University Hospital, Oslo, Norway.
With the emergence of large-scale Cap Analysis of Gene Expression (CAGE) datasets 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 genomic 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 provided by the user or selected from ∼1300 mammalian samples from the FANTOM5 project with pre-computed TFBS predicted with JASPAR TF binding profiles. The tool helps power insights into the 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 CONTACTS: anthony.mathelier@ncmm.uio.no or wyeth@cmmt.ubc.ca SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
References
Nucleic Acids Res. 2016 Jan 4;44(D1):D110-5
[PMID: 26531826]
