A genome-wide cis-regulatory element discovery method based on promoter sequences and gene co-expression networks

Zhen Gao, Ruizhe Zhao, Jianhua Ruan

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

    Abstract

    Deciphering cis-regulatory networks has become an attractive yet challenging task. This paper presents a simple model for cis-regulatory network discovery which aims to avoid most of the common problems of previous approaches. Using promoter sequences and gene co-expression profiles as input, rather than clustering the genes by the co-expression data, it includes neighborhood co-expression information for each individual gene from the co-expression data, thereby overcoming the disadvantages of current clustering based models which miss specific information for individual genes. Applications on Saccharomyces cerevisiae have shown a good prediction accuracy, which outperforms a phylogenetic footprinting approach. In addition, the top dozens of discovered gene-motif regulatory clusters are evidently functionally coregulated.

    Original languageEnglish (US)
    Title of host publicationProceeding of the 2012 ACM Research in Applied Computation Symposium, RACS 2012
    Pages74-75
    Number of pages2
    DOIs
    StatePublished - Dec 1 2012
    Event2012 ACM Research in Applied Computation Symposium, RACS 2012 - San Antonio, TX, United States
    Duration: Oct 23 2012Oct 26 2012

    Publication series

    NameProceeding of the 2012 ACM Research in Applied Computation Symposium, RACS 2012

    Conference

    Conference2012 ACM Research in Applied Computation Symposium, RACS 2012
    Country/TerritoryUnited States
    CitySan Antonio, TX
    Period10/23/1210/26/12

    Keywords

    • Cis-regulatory element discovery
    • Gene co-expression networks
    • Promoter sequences

    ASJC Scopus subject areas

    • Computational Theory and Mathematics

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