Identification of over-represented combinations of transcription factor binding sites in sets of co-expressed genes

Shao Shan Huang, Debra L. Fulton, David J. Arenillas, Paul Perco, Shannan J. Ho Sui, James R. Mortimer, Wyeth W. Wasserman

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

Transcription regulation is mediated by combinatorial interactions between diverse trans-acting proteins and arrays of cis-regulatory sequences. Revealing this complex interplay between transcription factors and binding sites remains a fundamental problem for understanding the flow of genetic information. The oPOSSUM analysis system facilitates the interpretation of gene expression data through the analysis of transcription factor binding sites shared by sets of co-expressed genes. The system is based on cross-species sequence comparisons for phylogenetic footprinting and motif models for binding site prediction. We introduce a new set of analysis algorithms for the study of the combinatorial properties of transcription factor binding sites shared by sets of co-expressed genes. The new methods circumvent computational challenges through an applied focus on families of transcription factors with similar binding properties. The algorithm accurately identifies combinations of binding sites over-represented in reference collections and clarifies the results obtained by existing methods for the study of isolated binding sites.

Original languageEnglish (US)
Title of host publicationProceedings of the 4th Asia-Pacific Bioinformatics Conference, APBC 2006
Pages247-256
Number of pages10
StatePublished - Dec 1 2006
Event4th Asia-Pacific Bioinformatics Conference, APBC 2006 - Taipei, Taiwan, Province of China
Duration: Feb 13 2006Feb 16 2006

Publication series

NameSeries on Advances in Bioinformatics and Computational Biology
Volume3
ISSN (Print)1751-6404

Other

Other4th Asia-Pacific Bioinformatics Conference, APBC 2006
CountryTaiwan, Province of China
CityTaipei
Period2/13/062/16/06

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ASJC Scopus subject areas

  • Bioengineering
  • Information Systems

Cite this

Huang, S. S., Fulton, D. L., Arenillas, D. J., Perco, P., Ho Sui, S. J., Mortimer, J. R., & Wasserman, W. W. (2006). Identification of over-represented combinations of transcription factor binding sites in sets of co-expressed genes. In Proceedings of the 4th Asia-Pacific Bioinformatics Conference, APBC 2006 (pp. 247-256). (Series on Advances in Bioinformatics and Computational Biology; Vol. 3).