FlyBase:GSEA

Gene Set Enrichment Tools

Some examples of GSEA tools with links and information. 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