This application performs gene set enrichment analysis using
INDRA CoGEx, an automatically assembled biomedical knowledge graph
consisting of causal, ontological, and property relationships,
as well as relationships representing data. Given a list of genes
as input the application ranks and lists GO terms, Reactome
pathways, WikiPathway pathways, as well as upstream or downstream
biological entities (e.g., genes/proteins, small molecules, biological
processes) with respect to the input genes. Ranking
is based on the overlap between the input genes and the gene sets
corresponding to each listed term (e.g., the genes annotated
with a given GO term or the genes that are part of a given
Reactome pathway). p-values are calculated using Fisher's exact
test with different options available to adjust for multiple hypothesis testing.
The corresponding REST API endpoint for this analysis is
/api/discrete_analysis. You can find it on the API
Docs under the section 'Analysis Queries'.