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

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

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.

MeSH terms

  • Binding Sites
  • Computational Biology*
  • High-Throughput Nucleotide Sequencing
  • Humans
  • Nucleotide Motifs*
  • Regulatory Sequences, Nucleic Acid
  • Software*
  • Transcription Factors
  • Transcription Initiation Site*

Substances

  • Transcription Factors