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Bioinformatics. 2016 Sep 15;32(18):2858-60. doi: 10.1093/bioinformatics/btw337. Epub 2016 Jun 9.

CAGEd-oPOSSUM: motif enrichment analysis from CAGE-derived TSSs.

Author information

1
Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, BC V5Z 4H4, Canada.
2
Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan RIKEN Omics Science Center, Yokohama, Kanagawa 230-0045 Japan.
3
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.
4
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.
5
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.

Abstract

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.

PMID:
27334471
PMCID:
PMC5018375
DOI:
10.1093/bioinformatics/btw337
[Indexed for MEDLINE]
Free PMC Article

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