DBRF-MEGN method: An algorithm for inferring gene regulatory networks from large-scale gene expression profiles

Abstract

The difference-based regulation finding-minimum equivalent gene network (DBRF-MEGN) method is an algorithm for inferring gene regulatory networks from gene expression profiles corresponding to gene perturbations. In this method, gene regulatory networks are modeled as signed directed graphs, and the most parsimonious graphs consistent with gene expression profiles are deduced by using a graph theoretical procedure. The method is applicable to large-scale gene expression profiles, and gene regulatory networks deduced by the method are highly consistent with gene regulations identified through classic small-scale experiments in genetics and cell biology. Free software for the method is available and runs under Windows or Linux platforms on a typical IBM-compatible personal computer. The DBRF-MEGN method will provide invaluable information for basic biology and drug discovery. © 2007 Humana Press Inc.