Skip to main content

Table 5 Functional enrichment analysis results. The 25 GO terms with the smallest Benjamini Hochberg (BH) adjusted p-values were selected for each cluster. The lists were then reduced to include only the most specific subclass for each ontology. All GO terms had a BH adjusted p-value < 0.01

From: A comparison of methods for multiple degree of freedom testing in repeated measures RNA-sequencing experiments

GO Term

Description

# Genes in Set

# Genes in Cluster

# Expected

Fold Enrichment

Cluster 3

GO:0002523

leukocyte migration involved in inflammatory response

12

6

0.30

20.00

GO:0050729

positive regulation of inflammatory response

86

13

2.15

6.05

GO:0051092

positive regulation of NF-kappaB transcription factor activity

136

16

3.40

4.71

GO:1990266

neutrophil migration

79

12

1.98

6.06

GO:0002755

MyD88-dependent toll-like receptor signaling pathway

33

7

0.83

8.43

GO:0045623

negative regulation of T-helper cell differentiation

14

5

0.35

14.29

GO:0060142

regulation of syncytium formation by plasma membrane fusion

14

5

0.35

14.29

GO:0071260

cellular response to mechanical stimulus

61

9

1.53

5.88

GO:0060396

growth hormone receptor signaling pathway

16

5

0.40

12.50

GO:0032651

regulation of interleukin-1 beta production

68

9

1.70

5.29

GO:0032695

negative regulation of interleukin-12 production

17

5

0.43

11.63

GO:0071354

cellular response to interleukin-6

28

6

0.70

8.57

Cluster 5

GO:0006958

complement activation, classical pathway

83

40

2.11

18.96

GO:0030449

regulation of complement activation

71

29

1.80

16.11

GO:0002377

immunoglobulin production

128

34

3.25

10.46

GO:0038096

Fc-gamma receptor signaling pathway involved in phagocytosis

117

29

2.97

9.76

GO:0006910

phagocytosis, recognition

54

21

1.37

15.33

GO:0050871

positive regulation of B cell activation

111

25

2.82

8.87

Cluster 6

GO:0006910

phagocytosis, recognition

54

9

0.22

40.91

GO:0006958

complement activation, classical pathway

83

9

0.34

26.47

GO:0006911

phagocytosis, engulfment

87

9

0.35

25.71

GO:0016584

nucleosome positioning

11

4

0.04

100.00

GO:0030261

chromosome condensation

35

5

0.14

35.71

GO:0045910

negative regulation of DNA recombination

37

4

0.15

26.67