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BioMed Research International
Volume 2013 (2013), Article ID 856325, 10 pages
http://dx.doi.org/10.1155/2013/856325
Research Article

DeGNServer: Deciphering Genome-Scale Gene Networks through High Performance Reverse Engineering Analysis

1Bioinformatics Lab, Plant Biology Division, Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK 73401, USA
2School of Forest Resources and Environmental Science, Michigan Technological University, 1400 Townsend Drive, Houghton, MI 49931, USA
3Department of Computer Science, Michigan Technological University, 1400 Townsend Drive, Houghton, MI 49931, USA

Received 22 August 2013; Accepted 1 October 2013

Academic Editor: Zhongming Zhao

Copyright © 2013 Jun Li 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

Analysis of genome-scale gene networks (GNs) using large-scale gene expression data provides unprecedented opportunities to uncover gene interactions and regulatory networks involved in various biological processes and developmental programs, leading to accelerated discovery of novel knowledge of various biological processes, pathways and systems. The widely used context likelihood of relatedness (CLR) method based on the mutual information (MI) for scoring the similarity of gene pairs is one of the accurate methods currently available for inferring GNs. However, the MI-based reverse engineering method can achieve satisfactory performance only when sample size exceeds one hundred. This in turn limits their applications for GN construction from expression data set with small sample size. We developed a high performance web server, DeGNServer, to reverse engineering and decipher genome-scale networks. It extended the CLR method by integration of different correlation methods that are suitable for analyzing data sets ranging from moderate to large scale such as expression profiles with tens to hundreds of microarray hybridizations, and implemented all analysis algorithms using parallel computing techniques to infer gene-gene association at extraordinary speed. In addition, we integrated the SNBuilder and GeNa algorithms for subnetwork extraction and functional module discovery. DeGNServer is publicly and freely available online.