MAGI-MS: Multiple seed-centric module discovery

Complex disorders manifest by the interaction of multiple genetic and environmental factors. Through the construction of genetic modules that consist of highly co-expressed genes, it is possible to identify genes that participate in common biological pathways relevant to specific phenotypes. We have previously developed tools MAGI and MAGI-S for genetic module discovery by incorporating co-expression and protein-interaction networks. Here we introduce an extension to MAGI-S, denoted as Merging Affected Genes into Integrated Networks - Multiple Seeds (MAGI-MS), that permits the user to further specify a disease pathway of interest by selecting multiple seed genes likely to function in the same molecular mechanism. By providing MAGI-MS with pairs of seed genes involved in processes underlying certain classes of neurodevelopmental disorders, such as epilepsy, we demonstrate that MAGI-MS can reveal modules enriched in genes relevant to chemical synaptic transmission, glutamatergic synapse, and other functions associated with the provided seed genes. Availability and implementationMAGI-MS is free and is available at: https://github.com/jchow32/MAGI-MS