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

Nucleic acids research | 2005

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 RIS Download

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Associated grants

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

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This is a list of tools and resources that we have found mentioned in this publication.


oPOSSUM (tool)

RRID:SCR_010884

A web-based system for the detection of over-represented conserved transcription factor binding sites and binding site combinations in sets of genes or sequences.

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ThermoFisher Polar Series Accel 500 LC Recirculating Chiller (tool)

RRID:SCR_020587

Chiller that offers 500 watts of cooling, with a working temperature range of 10� to 80�C

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