Skip to main content

Table 2 Top significant Gene Ontology categories for the MEF Ahr-/- dataset

From: Intensity-based hierarchical Bayes method improves testing for differentially expressed genes in microarray experiments

Top 10 GO t-test FOLD SMT IBMT
1 Extracellular space (77) Extracellular (91) Extracellular (90) Extracellular (92)
2 Extracellular (84) Extracellular space (82) Extracellular space (81) Response to biotic stimulus (39)
3 Integrin binding (5) Signal transducer activity (67) Receptor binding (27) Extracellular space (80)
4 Spermine/Spermidine biosynthesis (3) Organogenesis (38) Chemoattractant activity (8) Response to external stimulus (46)
5 Carboxy peptidase activity (6) Chemoattractant activity (7) Signal transducer activity (68) Defense response (34)
6 Spermidine metabolism (3) Receptor binding (24) Response to biotic stimulus (33) Signal transducer activity (68)
7 Polyamine biosynthesis (3) Histogenesis and organogenesis (9) Chemokine receptor binding/activity (7) Chemoattractant activity (8)
8 Receptor binding (22) Morphogenesis (39) Integrin binding (5) Immune response (27)
9 Adenosylmethionine decarboxylase activity (2) Serine-type endopeptidase inhibitor activity (9) G-protein-coupled receptor binding (7) Response to pest/pathogen/parasite (19)
10 Spermine metabolism (3) glycosaminoglycan binding (7) Spermine/Spermidine biosynthesis (3) Chemokine receptor binding/activity (7)
# Bonf<0.1 6 8 13 17
# genes ↑ 92 142 135 144
  1. Top ten categories for each of the four compared methods: magnitude of fold change, simple t-test, SMT, and IBMT. The IBMT method resulted in both the highest number of significant categories using a 0.10 Bonferroni-adjusted p-value cut-off, as well as the highest number of genes in a significant category.