About PANGEA
(PAthway, Network and Gene-set Enrichment Analysis) A Multi-Species Enrichment Tool
Gene Set Enrichment Analysis (GSEA) is a computational method used to examine gene lists to highlight common biological properties. Input gene lists are typically from high-throughput screens or analyses such as RNAi, microarray or proteomics. GSEA is used to show statistically significant over- or under-represented genes classes within the input gene list(s) by testing against gene sets assembled using prior knowledge. Annotation of biological functions using the Gene Ontology (GO) is often used as a gene set classifier, but sets can be built from any assembled data that divides genes into classes based on shared properties (e.g. phenotypes, expression patterns, disease involvement, or pathway membership).
The visualizations of enrichment results are enhanced by providing users with the option to view a gene set and gene relationships in a network view. PANGEA also allows users to upload multiple gene lists and helps them compare GSEA results quickly.
View Tutorial Slidedeck
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Gene Set Details
| Geme set | Gene set group | Source | Release 2025 |
|---|---|---|---|
| Gene Ontology sets
|
Using GO hierarchy | GO | 8 species |
| Direct GO term only | GO | 8 species | |
| GO slim1 | GO | 8 species | |
| GO slim2 | GO | 8 species | |
| Excluding high-throughput experiments | GO | 6 species except tick and mosquito | |
| Experimental data only | GO | 6 species except tick and mosquito | |
| Gene group collections
|
DRSC GLAD gene group | DRSC | fly |
| FlyBase gene group | FlyBase | fly | |
| HGNC gene group | HUGO | human | |
| Gene group collections
|
DRSC PathON signaling pathway core components | DRSC | fly |
| DRSC PathON signaling pathway target genes | DRSC | fly | |
| FlyBase signaling pathway | FlyBase | fly | |
| FlyBase metabolic pathway | FlyBase | fly | |
| KEGG pathway | KEGG | 8 species | |
| PANTHER pathway | PantherDB | 8 species | |
| REACTOME pathway | Reactome | 6 species except tick and mosquito | |
| Protein annotation
|
COMPLEAT protein complex (literature) | DRSC | fly, human |
| COMPLEAT protein complex (predicted) | DRSC | fly, human | |
| COMPLEAT2 protein complex (literature) | DRSC | 5 species, except worm, tick and mosquito | |
| EBI complex portal | EBI | 6 species except tick and mosquito | |
| Phenotype
|
FlyBase phenotype for classical alleles | FlyBase | fly |
| Disease annotation AGR | AGR | 6 species except tick and mosquito | |
| Expression
|
Preferred tissue (modEncode RNA_seq) | DRSC | fly |
| Preferred tissue (FlyCellAtlas) | DRSC | fly | |
| Expression annotation AGR | AGR | 5 species, except human, tick and mosquito |
Versions
Version Details
- Version 1 beta 1 (Feb 2023)
- Version 1.0.1 (July 2024) - minor bug fix to group names display on heatmap
- Version 2 (Nov 2025) - Added two new species (tick and mosquito) and added new gene sets (Preferred tissue (FlyCellAtlas), FlyBase metabolic pathway and COMPLEAT2 protein complex (literature))