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
Volume3
StatePublished - Dec 1 2006
Event4th Asia-Pacific Bioinformatics Conference, APBC 2006 - Taipei, Taiwan, Province of China
Duration: Feb 13 2006Feb 16 2006

Other

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

Fingerprint

Transcription factors
Binding sites
Transcription Factors
Genes
Binding Sites
Transcription
Computational methods
Gene expression
Proteins

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 (Vol. 3, pp. 247-256)

Identification of over-represented combinations of transcription factor binding sites in sets of co-expressed genes. / Huang, Shao-Shan; Fulton, Debra L.; Arenillas, David J.; Perco, Paul; Ho Sui, Shannan J.; Mortimer, James R.; Wasserman, Wyeth W.

Proceedings of the 4th Asia-Pacific Bioinformatics Conference, APBC 2006. Vol. 3 2006. p. 247-256.

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

Huang, S-S, Fulton, DL, Arenillas, DJ, Perco, P, Ho Sui, SJ, Mortimer, JR & Wasserman, WW 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. vol. 3, pp. 247-256, 4th Asia-Pacific Bioinformatics Conference, APBC 2006, Taipei, Taiwan, Province of China, 2/13/06.
Huang S-S, Fulton DL, Arenillas DJ, Perco P, Ho Sui SJ, Mortimer JR et al. 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. Vol. 3. 2006. p. 247-256
Huang, Shao-Shan ; Fulton, Debra L. ; Arenillas, David J. ; Perco, Paul ; Ho Sui, Shannan J. ; Mortimer, James R. ; Wasserman, Wyeth W. / Identification of over-represented combinations of transcription factor binding sites in sets of co-expressed genes. Proceedings of the 4th Asia-Pacific Bioinformatics Conference, APBC 2006. Vol. 3 2006. pp. 247-256
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