Inferring Subnetworks from Perturbed Expression Profiles

D. Pe'er, A. Regev, G. Elidan, and N. Friedman

9th Inter. Conf. on Intelligent Systems for Molecular Biology (ISMB), 2001. Appeared in Bioinformatics 17, suppl. 1 S215-24, 2001.
Recipient of the Best Paper Award

Web Supplement


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 substructures 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.