Epistasis Blog

From the Computational Genetics Laboratory at Dartmouth Medical School (www.epistasis.org)

Monday, March 11, 2013

ViSEN: Methodology and software for visualization of statistical epistasis networks

This is a short paper describing our new ViSEN software. This builds on work from the previous few posts on detecting three-way epistasis. Our ViSEN software package is freely available from sourceforge.

Hu T, Chen Y, Kiralis JW, Moore JH. ViSEN: Methodology and Software for Visualization of Statistical Epistasis Networks. Genet Epidemiol., in press 2013 [PubMed]

Abstract

The nonlinear interaction effect among multiple genetic factors, i.e. epistasis, has been recognized as a key component in understanding the underlying genetic basis of complex human diseases and phenotypic traits. Due to the statistical and computational complexity, most epistasis studies are limited to interactions with an order of two. We developed ViSEN to analyze and visualize epistatic interactions of both two-way and three-way. ViSEN not only identifies strong interactions among pairs or trios of genetic attributes, but also provides a global interaction map that shows neighborhood and clustering structures. This visualized information could be very helpful to infer the underlying genetic architecture of complex diseases and to generate plausible hypotheses for further biological validations. ViSEN is implemented in Java and freely available at https://sourceforge.net/projects/visen/.


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