SourceSet: A graphical model approach to identify primary genes in perturbed biological pathways.

ABSTRACT: Topological gene-set analysis has emerged as a powerful means for omic data interpretation. Although numerous methods for identifying dysregulated genes have been proposed, few of them aim to distinguish genes that are the real source of perturbation from those that merely respond to the signal dysregulation. Here, we propose a new method, called SourceSet, able to distinguish between the primary and the secondary dysregulation within a Gaussian graphical model context. The proposed method compares gene expression profiles in the control and in the perturbed condition and detects the differences in both the mean and the covariance parameters with a series of likelihood ratio tests. The resulting evidence is used to infer the primary and the secondary set, i.e. the genes responsible for the

SUBMITTER: Salviato E 

PROVIDER: S-EPMC6834292 | biostudies-literature | 2019 Oct

REPOSITORIES: biostudies-literature