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MAGI-MS: multiple seed-centric module discovery
Abstract
Summary
Complex disorders manifest by the interaction of multiple genetic and environmental factors. Through the construction of genetic modules that consist of highly coexpressed 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 coexpression and protein interaction networks. Here, we introduce an extension to MAGI-S, denoted as Merging Affected Genes into Integrated Networks-Multiple Seeds (MAGI-MS), which 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 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 implementation
MAGI-MS is free and available at https://github.com/jchow32/MAGI-MS.Supplementary information
Supplementary data are available at Bioinformatics Advances online.Many UC-authored scholarly publications are freely available on this site because of the UC's open access policies. Let us know how this access is important for you.