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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.