topologyGSA

Using Gaussian graphical models we propose a novel approach to perform pathway analysis using gene expression. Given the structure of a graph (a pathway) we introduce two statistical tests to compare the mean and the concentration matrices between two groups. Specifically, these tests can be performed on the graph and on its connected components (cliques).

Massa, M.S., Chiogna, M. and Romualdi, C. Massa, Maria Sofia, Monica Chiogna, and Chiara Romualdi. “Gene set analysis exploiting the topology of a pathway, BMC system biology, 2010 Dec; 4(1):1-5.