FlyBase:GSEA
Gene Set Enrichment Tools
Some examples of GSEA tools with links and information. It is recommended that users conduct their GSEA with >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 |