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The Scientific World Journal
Volume 2013 (2013), Article ID 197406, 9 pages
http://dx.doi.org/10.1155/2013/197406
Research Article

A Local Genetic Algorithm for the Identification of Condition-Specific MicroRNA-Gene Modules

Department of Bioengineering, University of Illinois at Chicago, Chicago, IL 60607, USA

Received 12 November 2012; Accepted 17 December 2012

Academic Editors: R. Jiang, W. Tian, J. Wan, and X. Zhao

Copyright © 2013 Wenbo Mu et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract

Transcription factor and microRNA are two types of key regulators of gene expression. Their regulatory mechanisms are highly complex. In this study, we propose a computational method to predict condition-specific regulatory modules that consist of microRNAs, transcription factors, and their commonly regulated genes. We used matched global expression profiles of mRNAs and microRNAs together with the predicted targets of transcription factors and microRNAs to construct an underlying regulatory network. Our method searches for highly scored modules from the network based on a two-step heuristic method that combines genetic and local search algorithms. Using two matched expression datasets, we demonstrate that our method can identify highly scored modules with statistical significance and biological relevance. The identified regulatory modules may provide useful insights on the mechanisms of transcription factors and microRNAs.