Inferring subnetworks from perturbed expression profiles

Dana Pe'er*, Aviv Regev, Gal Elidan, Nir Friedman

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

383 Scopus citations

Abstract

Genome-wide expression profiles of genetic mutants provide a wide variety of measurements of cellular responses to perturbations. Typical analysis of such data identifies genes affected by perturbation and uses clustering to group genes of similar function. In this paper we discover a finer structure of interactions between genes, such as causality, mediation, activation, and inhibition by using a Bayesian network framework. We extend this framework to correctly handle perturbations, and to identify significant subnetworks of interacting genes. We apply this method to expression data of S. cerevisiae mutants and uncover a variety of structured metabolic, signaling and regulatory pathways.

Original languageAmerican English
Pages (from-to)S215-S224
JournalBioinformatics
Volume17
Issue numberSUPPL. 1
DOIs
StatePublished - 2001

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