- Gene Ontology (GO) Enrichment Tools
- General Gene List Enrichment Tools
- Enrichr - can provide gene symbols, with or without weights
- WebGestalt
- Generalized tool covering many different functional databases
- DAVID
- functional enrichment tool provided by the NIH
- provides GO, KEGG, etc. enrichment analysis
- T-profiler
- only valid for analyzing yeast gene lists
- ConceptGen
- Other GO Enrichment Tools
- FIDEA - provides functional enrichment for GO, KEGG, and Interpro for human, mouse, fly, zebrafish, and yeast
- IPA (Ingenuity Pathway Analysis)
- commercial program curating information about genes, metabolites, etc.
Other Systems-Level Analysis Tools (No Upstream Filtering Necessary):
- Gene Set Enrichment Analysis (GSEA)
- very popular tool from the Broad Institute that analyzes data from MSigDB
- Reactome enrichment analysis - Reactome is an open-source pathway database
- ErmineJ
- PAGE
- LRpath
- GSVA
Posts
Very nice resource, thank you very much. I'll recommend it to my colleagues.
ReplyDeleteFor Gene Expression analysis, there is also a tool in the Reactome database: http://www.reactome.org/ReactomeGWT/entrypoint.html#ExpressionDataUploadPage
Good suggestion! I will add a link in this section for Reactome!
ReplyDeleteVery informative summary!
ReplyDeleteFor NGS analysis you could mention FIDEA (http://www.biocomputing.it/fidea)
The FIDEA server allows the user to directly input the results of a differential expression analysis and it performs
the enrichment analysis considering the upregulated and downregulated genes both together and separately.
Thanks for the suggestion - and congrats on your publication in NAR!
ReplyDeleteThank you for the congrats and the insertion!
ReplyDeleteA little thing, the correct link for FIDEA is http://www.biocomputing.it/fidea (and not cassandra.med.uniroma1.it/fidea).
Thanks again.