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Genome Biol. 2004;5(4):R29. Epub 2004 Mar 30.

Enriching for direct regulatory targets in perturbed gene-expression profiles.

Author information

  • 1Department of Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA.

Abstract

Here we build on a previously proposed algorithm to infer direct regulatory relationships using gene-expression profiles from cells in which individual genes are deleted or overexpressed. The updated algorithm can process networks containing feedback loops, incorporate positive and negative regulatory relationships during network reconstruction, and utilize data from double mutants to resolve ambiguous regulatory relationships. When applied to experimental data the reconstruction procedure preferentially retains direct transcription factor-target relationships.

PMID:
15059262
[PubMed - indexed for MEDLINE]
PMCID:
PMC395788
Free PMC Article

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