Table 1 Comparison of resources providing analysis methods and accessibility
From: Reactome pathway analysis: a high-performance in-memory approach
Resource | Analysis methods | Online tool | Programmatic access | Processing time | ||||
|---|---|---|---|---|---|---|---|---|
Hippocampal atrophy - 79 genesa | Migraine disorder - 644 genesb | Parkinson’s disease - 1492 genesc | Multiple sclerosis - 2570 genesd | Inflammatory bowel disease - 4110 genese | ||||
PANTHER | ORA | ✔ | – | ~2 s | ~4 s | ~6 s | ~8 s | ~12 s |
Consensus PathDB | ORA | ✔ | SOAP/WSDL | ~1 min | ~1 min | ~3 min | ~3 min | ~1 min |
DAVID | ORA | ✔ | SOAP/WSDL | ~4 s | ~4 s for conversion of official gene ids to 7498 DAVID ids. Analysis not performed - sample size limitation | ~5 s for conversion of official gene ids to 17272 DAVID ids. Analysis not performed - sample size limitation | ~8 s for conversion of official gene ids to 29420 DAVID ids. Analysis not performed - sample size limitation | Not performed - sample size limitation |
GSEA | ORA | – | – | – | – | – | – | |
REACTOME v1.0 | ORA | ✔ | – | ~2 min | ~7 min | ~12 min | ~19 min | ~25 min |
REACTOME v2.0 | ORA | ✔ | REST | ~1 s | ~1 s | ~2 s | ~2 s | ~3 s |