topologyGSA: an R package for Gene Set Analysis Exploiting Pathways Topology

We present the R package topologyGSA for genes sets analysis that exploits the known structure of relations between genes contained in pathways. The package contains tools for performing a multivariate analysis of sets of genes by using Gaussian graphical models, as described in Massa et al (2010). In particular, given gene expression data deriving from two experimental conditions and a pathway with the structure of the genes, the package is able to test the strength of the relations induced by the functional links and the differential expression of the pathway. It also identifies components of the pathway that behave differently in the given experimental conditions and highlight them directly in the graph.