Find biomedical concepts enriched for a list of genes or associations between concepts based on overlapping genes.

Launch Concept Gen via

User Guide
Tech Support

ConceptGen is an open-source gene set enrichment testing and concept mapping tool. This web-based tool can be used both to identify biological gene sets (called concepts) enriched with differentially expressed genes (or any other user-identified gene list), and to explore networks of relationships among biological concepts from diverse biological sources. You can either upload a list of human Entrez Gene IDs or gene symbols with or without a background gene set, or query from among the pre-built concepts. You also have the option of using the compound converter tool to convert one or more compounds/metabolites to their associated enzymes for upload.

Using a private account, you can identify associations among multiple user-uploaded gene sets. From the Explorer results page, you can export enrichment results to a spreadsheet, explore relationships with the network graph view, and use the heatmap view to visualize the relationships among a large number of genes and concepts. You can also link to concept data sources, MiMI gene pages, and MiMI interactions network view.

ConceptGen integrates data from diverse biological sources to form the following current list of 14 concept types: GO biological process, GO molecular function, GO cellular component, KEGG pathway, Biocarta pathway, Panther pathway, Drug Bank, Transfac, MiRBase, OMIM, pFAM, Gene Expression, Protein interactions (MiMI), and MeSH. The database currently consists of ~18,000 concepts, each with 5 or more assigned genes. Gene expression concepts were derived from public Affymetrix data downloaded from NCBI's gene expression omnibus (GEO) and analyzed using RMA normalization and an empirical Bayes testing method with our custom-built analysis pipeline.


Sartor MA, Mahavisno V, Keshamouni VG, Cavalcoli J, Wright Z, Karnovsky A, Kuick R, Jagadish HV, Mirel B, Weymouth T, Athey B, Omenn GS. ConceptGen: a gene set enrichment and gene set relation mapping tool. Bioinformatics. 2010 Feb 15.