Fast calculation of pairwise mutual information for gene regulatory network reconstruction

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• 作者：Peng Qiu ; Andrew J. Gentles ; Sylvia K. Plevritis
• 关键词：Mutual information ; Gene regulatory network ; Microarray
• 刊名：Computer Methods and Programs in Biomedicine
• 出版年：2009
• 出版时间：May 2009
• 年：2009
• 卷：94
• 期：2
• 页码：177-180
• 全文大小：463 K

文摘

We present a new software implementation to more efficiently compute the mutual information for all pairs of genes from gene expression microarrays. Computation of the mutual information is a necessary first step in various information theoretic approaches for reconstructing gene regulatory networks from microarray data. When the mutual information is estimated by kernel methods, computing the pairwise mutual information is quite time-consuming. Our implementation significantly reduces the computation time. For an example data set of 336 samples consisting of normal and malignant B-cells, with 9563 genes measured per sample, the current available software for ARACNE requires 142 hours to compute the mutual information for all gene pairs, whereas our algorithm requires 1.6 hours. The increased efficiency of our algorithm improves the feasibility of applying mutual information based approaches for reconstructing large regulatory networks.