Table 1 Comparison of GO-2D with related software
From: GO-2D: identifying 2-dimensional cellular-localized functional modules in Gene Ontology
| Â | Onto-Express | FatiGO | GoMiner | GOstat | GO-2D |
|---|---|---|---|---|---|
Analysis scope | 3 single categories | 3 single categories | 3 single categories | 3 single categories | Combined categories |
Correction for multiple tests | Šidák, Holm, Bonferroni, FDR | Step-down minP, FDR [16, 31] | Relative enrichment | Holm, FDR [16] | Bonferroni, FDR [16] |
Statistical Analysis | Hypergeometric, Binomial,χ2, Fisher's exact test, | Fisher's exact test | Fisher's exact test | χ2, Fisher's exact test, | Hypergeometric, Binomial |
Visualization | Flata, Tree | Flata, Tree | Tree, DAG | Flata | Tree, DAG |
Application | Web | Web | Stand-alone | Web | Stand-alone |