topologyGSA

swMATH15178CRANtopologyGSAMaRDI QIDQ27071

Gene Set Analysis Exploiting Pathway Topology

Sofia Massa

Last update: 25 September 2023

Software version identifier: 1.4.7, 1.0.2, 1.0.3, 1.0, 1.1.0, 1.2.0, 1.2.1, 1.4.0, 1.4.1, 1.4.2, 1.4.3, 1.4.4, 1.4.5, 1.4.6, 1.5.0

Source code repository: https://github.com/cran/topologyGSA

Copyright license: GNU General Public License, version 3.0

Description

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). The package is based on the method described in Massa M.S., Chiogna M., Romualdi C. (2010) <doi:10.1186/1752-0509-4-121>.

Cites work

• Gene set analysis exploiting the topology of a pathway