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Gene Set Enrichment Tools

Some examples of GSEA tools with links and information. A list of more GSEA tools can be found here.

It is recommended that users conduct their GSEA with more than one tool as all have different features, use statistically significant results and compare the overlap between enriched sets to further interpretation. With any GSEA, there will be genes within the analysis set that are not represented in the gene set libraries, e.g. genes that have very little characterisation. These may be of interest for further study, even though they are not in an enriched set.

Selected Gene Set Enrichment Tool Information

Tool Backronym Publication Enrichment sets Organism(s) ID conversion Multiple set enrichment available Parallel gene list analysis Custom background input Stats Visualisation Other features API Update Notes Help/tutorials
DAVID Database for Annotation, Visualization and Integrated Discovery PMID:35325185 Many (e.g. GO, interaction, domains, UniProt KeyWord, drug, human expression, disease, pathways) Large coverage Yes Yes No Yes p-value, Benjamini Bar chart and limited gene/term bin heat map; will also group bar charts in sets Manipulation of gene lists. Yes Updated ~twice yearly Updates Tutorial
Enrichr - PMID:33780170 Many (e.g. GO, disease, interaction, domains, phenotype, pathways), especially for human Enrichr Human & mouse, sites for Mod-specific sets: FlyEnrichr (D.mel), YeastEnrichr (S.cerevisiae), WormEnrichr (C. elegans), FishEnrichr (D. rerio) No Yes Yes No p-value, z-score Bar chart, table Analysis sharing feature. Other viewing features such as networks and gene-set similarity grid available for some set genes. Yes See New and Libraries Help center
GO term finder - PMID:15297299 GO Many (see dropdown menu) Yes No No Yes p-value, Bonferroni, FDR GO graph with heat map Can select to use regulates links in the GO. Select evidence codes to exclude (HTP not listed). Upload a custom gene association file. Open Source. No Updated with GO release (monthly) -
GO/PANTHER Gene Ontology; Protein ANalysis THrough Evolutionary Relationships PMID:34717010 GO, GO Slim sets, PANTHER protein class, Reactome Pathways Large coverage No No Yes Yes p-value, FDR, Enrichment, Bonferroni, Fisher's Exact or Binomial test Hierarchical viewer of enrichment table; some graphical representation: pie, bar chart Can select set and statical method No Updated with GO release (monthly) and PANTHER release -
g:Profiler/g:GOSt - PMID:31066453 GO, KEGG, REACTOME, WikiPathways, TRANSFAC, mirTarBase, Human Protein Atlas, CORUM, HPO Large coverage Yes Yes Yes Yes p-value, tailor-made algorithm g:SCS, Bonferroni, Benjamini-Hochberg. Interactive Manhattan plot, heat map Can select set and statical method, select to exclude electronic GO annotations and different gene sets to enrich for. Ortholog mapping R package Yes Regular updates News. Also has archived versions Documentation
GOrilla Gene Ontology enRIchment anaLysis and visuaLizAtion tool PMID:19192299 GO D. melanogaster, Arabidopsis, S.cerevisiae, C.elegans, zebrafish, human, mouse, rat No No No Yes p-value, FDR q-value (Benjamini and Hochberg), enrichment Heat map GO Graph view Certain stats can be customised. Can run MF, BP, CC the same time but output is separated No ? Usage Instructions
PANGEA PAthway, Network and Gene-set Enrichment Analysis PMID:37125646 GO, gene groups, pathways, disease, protein complexes, phenotype, expression D. melanogaster, C.elegans. zebrafish, human, mouse, rat Yes Yes Yes Yes p-value, Bonferroni, Benjamini-Hochberg, Benjamini-Yekutieli Heatmap, bar chart, network, dot plot Customisable tables, selectable sets and interactive, customisable visualisation tools. No Updated every two months About; Video tutorial
WebGestalt - PMID:31114916 GO, pathways, PANTHER, MSigDB, PTMs, phenotype, chromosomal location, co-expression Many (see dropdown list) No No No No p-value, FDR Table, bar chart, volcano plot and GO graph. Can select different methods of analysis: over-representation analysis, GSEA, Network-Topology based. GSEA for microarray data input, over-representation analysis for single GSEA or Network-topology based analysis (PPI network). Stand alone network viewer. Yes 2019 Manual