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
| Section | Gene sets | Source | Coverage |
| Gene Ontology sets
|
Using GO hierarchy (Flatten gene2GO based GO hierarchy) | ||
| GO Biological Processes | GO | all | |
| GO Cellular Component | GO | all | |
| GO Molecular Function | GO | all | |
| Direct GO term only (Direct gene2GO relationships) | |||
| Direct GO Biological Processes | GO | all | |
| Direct GO Cellular Component | GO | all | |
| Direct GO Molecular Function | GO | all | |
| Gene Ontology Subsets | Generic GO consortium subsets (GO slim1) | ||
| Generic GO Biological Process subset (slim) | GO | all | |
| Generic GO Cellular Component subset (slim) | GO | all | |
| Generic GO Molecular Function subset (slim) | GO | all | |
| Drosophila GO subsets (GO slim2) | |||
| SLIM2 GO BP | FlyBase/Alliance | all | |
| SLIM2 GO CC | FlyBase/Alliance | all | |
| SLIM2 GO MF | FlyBase/Alliance | all | |
| Gene Ontology gene annotation subsets | Excluding high-throughput experiments | ||
| No HTP GO Biological Processes | GO | all | |
| No HTP GO Cellular Component | GO | all | |
| No HTP GO Molecular Function | GO | all | |
| Experimental data only | |||
| EXP GO Biological Processes | GO | all | |
| EXP GO Cellular Component | GO | all | |
| EXP GO Molecular Function | GO | all | |
| Other Gene Sets
|
Gene group collections | ||
| DRSC GLAD Gene Group | DRSC | fly | |
| FlyBase gene groups | FlyBase | fly | |
| HGNC | HGNC | human | |
| Pathway Resources | |||
| KEGG Pathway | KEGG | all | |
| REACTOME pathway | REACTOME | all | |
| PathON signaling pathway core components | DRSC | fly | |
| PathON signaling pathway target genes | DRSC | fly | |
| FlyBase signalling pathways | FlyBase | fly | |
| PANTHER pathway | PantherDB | fly | |
| Protein annotation | |||
| COMPLEAT protein complex (literature) | DRSC | fly | |
| COMPLEAT protein complex (predicted) | DRSC | fly | |
| EBI complex portal | EBI | all | |
| Phenotype | |||
| FlyBase phenotype for classical alleles | FlyBase | fly | |
| Disease annotation Alliance | Alliance | all | |
| Expression | |||
| Preferred tissue (modEncode RNA_seq) | DRSC | fly | |
| Expression annotation Alliance | Alliance | all except human | |
Versions
Version Details
- Version 1 beta 1 (Feb 2023)