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
Externally publishedYes
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
CountryUnited 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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