Gene Set Analysis

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 minimum number of evidences, if using INDRA path-based analysis.
The minimum belief score, if using INDRA path-based analysis.
The alpha is the threshold for significance in the Fisher's exact test with which multiple hypothesis testing correction will be executed.
Paste your list of gene symbols, HGNC gene identifiers, or CURIEs here or click here to use an example list of human genes related to COVID-19.