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Citation
Kim, J., Cunningham, R., James, B., Wyder, S., Gibson, J.D., Niehuis, O., Zdobnov, E.M., Robertson, H.M., Robinson, G.E., Werren, J.H., Sinha, S. (2010). Functional characterization of transcription factor motifs using cross-species comparison across large evolutionary distances.  PLoS Comput. Biol. 6(1): e1000652.
FlyBase ID
FBrf0214903
Publication Type
Research paper
Abstract

We address the problem of finding statistically significant associations between cis-regulatory motifs and functional gene sets, in order to understand the biological roles of transcription factors. We develop a computational framework for this task, whose features include a new statistical score for motif scanning, the use of different scores for predicting targets of different motifs, and new ways to deal with redundancies among significant motif-function associations. This framework is applied to the recently sequenced genome of the jewel wasp, Nasonia vitripennis, making use of the existing knowledge of motifs and gene annotations in another insect genome, that of the fruitfly. The framework uses cross-species comparison to improve the specificity of its predictions, and does so without relying upon non-coding sequence alignment. It is therefore well suited for comparative genomics across large evolutionary divergences, where existing alignment-based methods are not applicable. We also apply the framework to find motifs associated with socially regulated gene sets in the honeybee, Apis mellifera, using comparisons with Nasonia, a solitary species, to identify honeybee-specific associations.

PubMed ID
PubMed Central ID
PMC2813253 (PMC) (EuropePMC)
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Secondary IDs
    Language of Publication
    English
    Additional Languages of Abstract
    Parent Publication
    Publication Type
    Journal
    Abbreviation
    PLoS Comput. Biol.
    Title
    PLoS Computational Biology
    Publication Year
    2005-
    ISBN/ISSN
    1553-7358 1553-734X
    Data From Reference
    Genes (20)