• Register
Forgot Password

If you have forgotten your password you can enter your email here and get a temporary password sent to your email.


Leaving Community

Are you sure you want to leave this community? Leaving the community will revoke any permissions you have been granted in this community.


oPOSSUM: identification of over-represented transcription factor binding sites in co-expressed genes.

Targeted transcript profiling studies can identify sets of co-expressed genes; however, identification of the underlying functional mechanism(s) is a significant challenge. Established methods for the analysis of gene annotations, particularly those based on the Gene Ontology, can identify functional linkages between genes. Similar methods for the identification of over-represented transcription factor binding sites (TFBSs) have been successful in yeast, but extension to human genomics has largely proved ineffective. Creation of a system for the efficient identification of common regulatory mechanisms in a subset of co-expressed human genes promises to break a roadblock in functional genomics research. We have developed an integrated system that searches for evidence of co-regulation by one or more transcription factors (TFs). oPOSSUM combines a pre-computed database of conserved TFBSs in human and mouse promoters with statistical methods for identification of sites over-represented in a set of co-expressed genes. The algorithm successfully identified mediating TFs in control sets of tissue-specific genes and in sets of co-expressed genes from three transcript profiling studies. Simulation studies indicate that oPOSSUM produces few false positives using empirically defined thresholds and can tolerate up to 50% noise in a set of co-expressed genes.

Pubmed ID: 15933209


  • Ho Sui SJ
  • Mortimer JR
  • Arenillas DJ
  • Brumm J
  • Walsh CJ
  • Kennedy BP
  • Wasserman WW


Nucleic acids research

Publication Data

June 3, 2005

Associated Grants

  • Agency: Canadian Institutes of Health Research, Id: 64231

Mesh Terms

  • Algorithms
  • Animals
  • Binding Sites
  • Databases, Nucleic Acid
  • Gene Expression Profiling
  • Gene Expression Regulation
  • Humans
  • Internet
  • Mice
  • NF-kappa B
  • Oligonucleotide Array Sequence Analysis
  • Promoter Regions, Genetic
  • Transcription Factors