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MAGI-MS: Multiple seed-centric module discovery
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Abstract
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 implementation
MAGI-MS is free and is available at:
https://github.com/jchow32/MAGI-MS
Title: MAGI-MS: Multiple seed-centric module discovery
Description:
Abstract
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 implementation
MAGI-MS is free and is available at:
https://github.
com/jchow32/MAGI-MS.
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