- 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
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