Along signal paths: an empirical gene set approach exploiting pathway topology.

ABSTRACT: Gene set analysis using biological pathways has become a widely used statistical approach for gene expression analysis. A biological pathway can be represented through a graph where genes and their interactions are, respectively, nodes and edges of the graph. From a biological point of view only some portions of a pathway are expected to be altered; however, few methods using pathway topology have been proposed and none of them tries to identify the signal paths, within a pathway, mostly involved in the biological problem. Here, we present a novel algorithm for pathway analysis clipper, that tries to fill in this gap. clipper implements a two-step empirical approach based on the exploitation of graph decomposition into a junction tree to reconstruct the most relevant signal path. In the fi

SUBMITTER: Martini P 

PROVIDER: S-EPMC3592432 | biostudies-literature | 2013 Jan

REPOSITORIES: biostudies-literature