Gene regulatory network inference using fused LASSO on multiple data sets.

ABSTRACT: Devising computational methods to accurately reconstruct gene regulatory networks given gene expression data is key to systems biology applications. Here we propose a method for reconstructing gene regulatory networks by simultaneous consideration of data sets from different perturbation experiments and corresponding controls. The method imposes three biologically meaningful constraints: (1) expression levels of each gene should be explained by the expression levels of a small number of transcription factor coding genes, (2) networks inferred from different data sets should be similar with respect to the type and number of regulatory interactions, and (3) relationships between genes which exhibit similar differential behavior over the considered perturbations should be favored. We demonstr

SUBMITTER: Omranian N 

PROVIDER: S-EPMC4750075 | biostudies-literature | 2016 Feb

REPOSITORIES: biostudies-literature