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Enriching for direct regulatory targets in perturbed gene-expression profiles

Susannah G Tringe13, Andreas Wagner2 and Stephanie W Ruby1*

Author Affiliations

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

2 Department of Biology, University of New Mexico, Albuquerque, NM 87131, USA

3 Current address: DOE Joint Genome Institute, 2800 Mitchell Drive, Bldg 400, Walnut Creek, CA 94596, USA

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Genome Biology 2004, 5:R29  doi:

Published: 30 March 2004


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.