oPOSSUM-3: advanced analysis of regulatory motif over-representation across genes or ChIP-Seq datasets

G3 (Bethesda). 2012 Sep;2(9):987-1002. doi: 10.1534/g3.112.003202. Epub 2012 Sep 1.


oPOSSUM-3 is a web-accessible software system for identification of over-represented transcription factor binding sites (TFBS) and TFBS families in either DNA sequences of co-expressed genes or sequences generated from high-throughput methods, such as ChIP-Seq. Validation of the system with known sets of co-regulated genes and published ChIP-Seq data demonstrates the capacity for oPOSSUM-3 to identify mediating transcription factors (TF) for co-regulated genes or co-recovered sequences. oPOSSUM-3 is available at http://opossum.cisreg.ca.

Keywords: ChIP-Seq; gene regulation; transcription; transcription factor binding sites (TFBS).

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Base Composition
  • Binding Sites
  • Chromatin Immunoprecipitation
  • Cilia / genetics
  • Computational Biology / methods*
  • High-Throughput Nucleotide Sequencing
  • Humans
  • Internet
  • Muscle, Skeletal / metabolism
  • Nematoda / genetics
  • Nucleotide Motifs*
  • Regulatory Sequences, Nucleic Acid*
  • Software*
  • Transcription Factors / metabolism


  • Transcription Factors