Gene regulatory network reconstruction using conditional mutual information

Abstract

The inference of gene regulatory network from expression data is an important area of research that provides insight to the inner workings of a biological system. The relevance-network-based approaches provide a simple and easily-scalable solution to the understanding of interaction between genes. Up until now, most works based on relevance network focus on the discovery of direct regulation using correlation coefficient or mutual information. However, some of the more complicated interactions such as interactive regulation and coregulation are not easily detected. In this work, we propose a relevance network model for gene regulatory network inference which employs both mutual information and conditional mutual information to determine the interactions between genes. For this purpose, we propose a conditional mutual information estimator based on adaptive partitioning which allows us to condition on both discrete and continuous random variables. We provide experimental results that demonstrate that the proposed regulatory network inference algorithm can provide better performance when the target network contains coregulated and interactively regulated genes. Copyright © 2008 K.-C. Liang and X.Wang.