ChiNet uncovers rewired transcription subnetworks in tolerant yeast for advanced biofuels conversion.

ABSTRACT: Analysis of rewired upstream subnetworks impacting downstream differential gene expression aids the delineation of evolving molecular mechanisms. Cumulative statistics based on conventional differential correlation are limited for subnetwork rewiring analysis since rewiring is not necessarily equivalent to change in correlation coefficients. Here we present a computational method ChiNet to quantify subnetwork rewiring by statistical heterogeneity that enables detection of potential genotype changes causing altered transcription regulation in evolving organisms. Given a differentially expressed downstream gene set, ChiNet backtracks a rewired upstream subnetwork from a super-network including gene interactions known to occur under various molecular contexts. We benchmarked ChiNet for its hi

SUBMITTER: Zhang Y 

PROVIDER: S-EPMC4482087 | biostudies-literature | 2015 May

REPOSITORIES: biostudies-literature