An integrative genomics approach to the reconstruction of gene networks in segregating populations

J. Zhu, P. Y. Lum, J. Lamb, D. GuhaThakurta, S. W. Edwards, R. Thieringer, J. P. Berger, M. S. Wu, J. Thompson, A. B. Sachs, E. E. Schadt

Research output: Contribution to journalArticlepeer-review

176 Scopus citations

Abstract

The reconstruction of genetic networks in mammalian systems is one of the primary goals in biological research, especially as such reconstructions relate to elucidating not only common, polygenic human diseases, but living systems more generally. Here we propose a novel gene network reconstruction algorithm, derived from classic Bayesian network methods, that utilizes naturally occurring genetic variations as a source of perturbations to elucidate the network. This algorithm incorporates relative transcript abundance and genotypic data from segregating populations by employing a generalized scoring function of maximum likelihood commonly used in Bayesian network reconstruction problems. The utility of this novel algorithm is demonstrated via application to liver gene expression data from a segregating mouse population. We demonstrate that the network derived from these data using our novel network reconstruction algorithm is able to capture causal associations between genes that result in increased predictive power, compared to more classically reconstructed networks derived from the same data.

Original languageEnglish
Pages (from-to)363-374
Number of pages12
JournalCytogenetic and Genome Research
Volume105
Issue number2-4
DOIs
StatePublished - 2004
Externally publishedYes

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