Human metabolic gene set collections

GSAM enables the generation of gene set collections (GSCs) from genome-scale metabolic models (GEMs) using the extractMetabliteGSC or extractSubsystemGSC functions.

For convenience, GSCs extracted from the latest version of the human genome-scale metabolic model Human-GEM are hosted on the GSAM GitHub repository as .gmt files. This facilitates the use of Human-GEM-derived GSCs for use in other packages (e.g., Piano or GSEA) without requiring GSAM or MATLAB.

The names of these GSCs indicate the version of Human-GEM from which they were extracted, as well as the format of the gene IDs (Ensembl ID or Gene Symbol).

Metabolite GSC

The metabolite .gmt files contain metabolite-gene associations extracted from Human-GEM, where each metabolite is a gene set. Each metabolite is associated with the genes encoding the reaction(s) involving that metabolite. Such a metabolite GSC is employed in the reporter metabolite approach.

Subsystem GSC

The subsystem .gmt files contain subsystem-gene associations extracted from Human-GEM, where each subsystem (metabolic pathway) is a gene set. Each subsystem is associated with the genes encoding the reaction(s) comprising that subsystem.