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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
  1. Comparison between different resources and whether they provide analysis methods which are accessible online (UX or programmatic access) and the average response time for a predefined sample. For the comparison of processing time, only the first column in the test sets -the gene identifiers- has been used. Datasets are available in
  2. a https://www.targetvalidation.org/disease/EFO_0005039/associations (accessed 13/07/2016)
  3. b https://www.targetvalidation.org/disease/EFO_0003821/associations (accessed 13/07/2016)
  4. c https://www.targetvalidation.org/disease/EFO_0002508/associations (accessed 13/07/2016)
  5. d https://www.targetvalidation.org/disease/EFO_0003885/associations (accessed 13/07/2016)
  6. e https://www.targetvalidation.org/disease/EFO_0003767/associations (accessed 13/07/2016)