Model-based identification of cis-acting elements from microarray data

Yunlong Liu, Milton W. Taylor, Howard J. Edenberg

Research output: Contribution to journalArticle

18 Citations (Scopus)

Abstract

Identification of transcriptional regulatory motifs continues to be a challenging problem in computational biology. We report a model-based procedure, MotifModeler, that uses global gene expression data to (1) identify cis-acting elements (CAE) that regulate gene expression under a given condition and (2) estimate the effects of the CAE on gene expression. MotifModeler repeatedly tests random subsets of all possible motifs of a given size and selects those that best fit a combinatorial model of the expression levels. We tested MotifModeler using data from a microarray experiment on the effects of interferon-α in peripheral blood monocytes. Focusing on 6-bp motifs, we predicted 16 stimulatory and 4 inhibitory motifs. Motifs were extended and compared to known binding sites in the TRANSFAC database using position-specific scoring matrices. Many predicted CAE match sites known to be involved in interferon action. MotifModeler demonstrated the potential to computationally identify CAE important in gene regulation.

Original languageEnglish (US)
Pages (from-to)452-461
Number of pages10
JournalGenomics
Volume88
Issue number4
DOIs
StatePublished - Oct 1 2006

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Gene Expression
Interferons
Position-Specific Scoring Matrices
Computational Biology
Monocytes
Binding Sites
Databases
Genes

Keywords

  • cis-acting elements
  • Gene expression
  • Gene regulation
  • Interferon
  • Microarrays
  • Transcription factors

ASJC Scopus subject areas

  • Genetics

Cite this

Model-based identification of cis-acting elements from microarray data. / Liu, Yunlong; Taylor, Milton W.; Edenberg, Howard J.

In: Genomics, Vol. 88, No. 4, 01.10.2006, p. 452-461.

Research output: Contribution to journalArticle

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