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Table 2 GO categories enriched for upregulated and downregulated genes

From: Characterisation of the global transcriptional response to heat shock and the impact of individual genetic variation

GO ID

Term

Annotated genes

Significant

Expected

Rank in downregulated genes

p value (FDR) for upregulated genes

p value (FDR) for downregulated genes

(A) Top GO categories enriched for upregulated genes

 GO:0009408

Response to heat

70

13

1.51

2483

5.7 × 10−8 (2.3 × 10−4)

0.87 (1)

 GO:0006986

Response to unfolded protein

97

15

2.09

2757

7.1 × 10−8 (2.7 × 10−4)

1 (1)

 GO:0006457

Protein folding

133

17

2.87

1600

1.7 × 10−7 (6.4 × 10−4)

0.52 (1)

 GO:0035966

Response to topologically incorrect protein

106

15

2.29

2368

2.4 × 10−7 (9.4 × 10−4)

0.81 (1)

 GO:0009266

Response to temperature stimulus

96

13

2.07

2257

2.5 × 10−6 (9.8 × 10−3)

0.76 (1)

 GO:0042026

Protein refolding

11

5

0.24

2758

6.7 × 10−6 (0.028)

1 (1)

 GO:0034605

Cellular response to heat

50

9

1.08

2759

8.6 × 10−6 (0.035)

1 (1)

 GO:0043618

Regulation of transcription from RNA polymerase II promoter in response to stress

35

7

0.76

1907

4.3 × 10−5 (0.18)

0.63 (1)

 GO:1900034

Regulation of cellular response to heat

26

6

0.56

2760

6.6 × 10−5 (0.27)

1 (1)

 GO:0043620

Regulation of DNA-templated transcription in response to stress

39

7

0.84

2008

9 × 10−5 (0.37)

0.67 (1)

(B) Top GO categories enriched for down regulated genes

 GO:0051225

Spindle assembly

37

6

0.82

1

1 (1)

5.4 × 10−4 (1)

 GO:0043207

Response to external biotic stimulus

342

20

7.59

2

0.63 (1)

1.6 × 10−3 (1)

 GO:0051707

Response to other organism

342

20

7.59

3

0.63 (1)

1.6 × 10−3 (1)

 GO:0045931

Positive regulation of mitotic cell cycle

64

7

1.42

4

1 (1)

2.1 × 10−3 (1)

 GO:0007049

Cell cycle

1037

45

23.02

5

0.69 (1)

2.2 × 10−3 (1)

 GO:0007143

Female meiotic division

10

3

0.22

6

1 (1)

2.3 × 10−3 (1)

 GO:0009607

Response to biotic stimulus

355

20

7.88

7

0.54 (1)

2.6 × 10−3 (1)

 GO:0032496

Response to lipopolysaccharide

128

10

2.84

8

0.49 (1)

3.3 × 10−3 (1)

 GO:1903047

Mitotic cell cycle process

552

27

12.26

9

0.78 (1)

3.7 × 10−3 (1)

 GO:0002237

Response to molecule of bacterial origin

134

10

2.98

10

0.52 (1)

4.6 × 10−3 (1)

 GO:0008219

Cell death

1022

43

22.69

11

4.3 × 10−3 (1)

4.9 × 10−3 (1)

  1. The most significant GO categories for differentially expressed genes following heat shock in LCLs are shown. Numbers of significant and expected genes shown, together with p values (Fisher’s exact test)