TINGe 1.062 / GeNA 0.1
TINGe (Tool for Inferring Networks of GEnes) is a parallel and multi-platform framework for reconstructing gene regulatory networks from large gene expression data. It uses parallel processing, information theoretic criteria and statistical testing to derive networks with thousands of genes from microarray sets with thousands of observations. TINGe has been used to reconstruct a whole-genome network of Arabidopsis thaliana from 3,546 microarray measurements, which comprises of 15,495 genes.
GeNA (GEne Networks Analyzer) is a tool that for a given set of “seed” genes uses gene ranking mechanism to extract subnetworks of genes with similar biological function. GeNA uses algorithm akin to the topic-sensitive PageRank and it has been implemented as a stand-alone tool and as a plugin for Cytoscape.
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Jaroslaw Zola, et al.
Parallel Information-Theory-Based Construction of Genome-Wide Gene Regulatory Networks
IEEE Transactions on Parallel and Distributed Systems. December 2010 (vol. 21 no. 12) pp. 1721-1733