Skip to main content

Table 2 Summary of the analytical approaches and choice of software for each group

From: Methods for interpreting lists of affected genes obtained in a DNA microarray experiment

Group Analytical tool Classa Key statistical method
University of Cordoba, Spain [25] ArrayUnlock [31] MEA Hypergeometric; Chi Square-test
  Ingenuity Pathway Analysis [32] SEA Fisher's exact test
Institute for Animal Health, Compton, UK [27] MAPPFinder/GenMAPP [14, 33, 34] SEA Z-score; Hypergeometric
Aarhus University, Denmark [24] LIMMA [35] SEA Wilcoxon
  TopGO [30] MEA Fisher's exact test; Kolmogorov Smirnoff
  Globaltest [36] GSEA Global test
  GIST [37] - support vector machine classification; kernel principal components analysis
Animal Breeding and Genomics Centre, Wageningen University, Wageningen, The Netherlands [23] AnnotationDbi [38] - -
  GOstats [39] SEA Hypergeometric
Animal Breeding and Genomics Centre, Animal Sciences Group, Lelystad, The Netherlands [28] Globaltest [36] GSEA Global test
  GOEAST [40] SEA Fisher's exact; Hypergeometric; Chi Square-test
INRA, Toulouse and Rennes [26] GOTM [41] SEA, GSEA Hypergeometric
  Pathway Studio [42] - Subnetwork Enrichment Analysis (SNEA), one-sided Mann-Whitney U-Test
  Ingenuity Pathway Analysis [32] SEA Fisher's exact test
  1. a SEA, singular enrichment analysis; GSEA, gene set enrichment analysis; MEA, modular enrichment analysis, as suggested by Huang et al [15]