Table 2 GO and pathway terms associated with differentially expressed APA sites following sleep deprivation/recovery

From: Sleep and diurnal alternative polyadenylation sites associated with human APA-linked brain disorders

GO description

size

overlap

expect

ratio

p-value

FDR

database

ZT6 vs R0

synaptic membrane

396

5

0.37

13.40

1.88E-05

1.79E-02

CC

neuron-to-neuron synapse

322

4

0.30

13.18

1.69E-04

4.52E-02

CC

postsynaptic specialization

327

4

0.31

12.98

1.80E-04

4.52E-02

CC

localization within membrane

130

3

0.12

24.48

2.14E-04

4.52E-02

BP

glutamatergic synapse

368

4

0.35

11.53

2.83E-04

4.52E-02

CC

phosphatase binding

143

3

0.13

22.26

2.83E-04

4.52E-02

MF

ZT10 vs R4

synaptic membrane

396

31

8.09

3.83

1.22E-10

1.17E-07

CC

glutamatergic synapse

368

26

7.51

3.46

3.52E-08

1.68E-05

CC

neuron-to-neuron synapse

322

23

6.58

3.50

1.86E-07

5.85E-05

CC

postsynaptic specialization

327

23

6.68

3.44

2.45E-07

5.85E-05

CC

regulation of trans-synaptic signaling

375

24

7.66

3.13

7.43E-07

1.42E-04

BP

neuron spine

182

16

3.72

4.30

9.83E-07

1.57E-04

CC

glutamate receptor signaling pathway

78

10

1.59

6.28

3.94E-06

5.38E-04

BP

regulation of synapse structure or activity

201

15

4.10

3.65

1.60E-05

1.91E-03

BP

synaptic transmission, glutamatergic

83

9

1.69

5.31

4.73E-05

5.02E-03

BP

regulation of neuron projection development

422

22

8.62

2.55

5.46E-05

5.22E-03

BP

localization within membrane

130

11

2.65

4.14

7.10E-05

6.17E-03

BP

behavior

464

22

9.48

2.32

2.15E-04

1.71E-02

BP

positive regulation of nervous system development

447

21

9.13

2.30

3.39E-04

2.41E-02

BP

protein exit from endoplasmic reticulum

31

5

0.63

7.90

3.76E-04

2.41E-02

BP

synapse organization

296

16

6.04

2.65

3.86E-04

2.41E-02

BP

axon part

389

19

7.94

2.39

4.03E-04

2.41E-02

CC

presynapse

489

22

9.99

2.20

4.44E-04

2.50E-02

CC

cell part morphogenesis

428

20

8.74

2.29

5.02E-04

2.52E-02

BP

dendrite development

189

12

3.86

3.11

5.06E-04

2.52E-02

BP

regulation of G protein-coupled receptor signaling pathway

91

8

1.86

4.30

5.35E-04

2.52E-02

BP

cell leading edge

276

15

5.64

2.66

5.53E-04

2.52E-02

CC

endoplasmic reticulum to cytosol transport

21

4

0.43

9.33

7.73E-04

3.23E-02

BP

excitatory synapse

54

6

1.10

5.44

7.78E-04

3.23E-02

CC

endocytosis

418

19

8.54

2.23

9.62E-04

3.83E-02

BP

forebrain development

295

15

6.02

2.49

1.09E-03

4.18E-02

BP

receptor metabolic process

127

9

2.59

3.47

1.17E-03

4.31E-02

BP

ZT10 vs R4

Pathway description

size

overlap

expect

ratio

p-value

FDR

database

mRNA surveillance pathway

95

11

1.81

6.07

1.83E-06

3.40E-03

KEGG

  1. GO and pathway analyses were performed on lists of genes with ≥2 APA sites that exhibited differential expression of at least 1 APA site following sleep deprivation/recovery compared to controls using the over-representation analysis function of the online web tool WebGestalt. GO or pathway description is followed by the size (total number of genes that the term is comprised of), overlap (number of input genes matching the term), expect (number of input genes expected to match by chance), ratio (number of actual/expected matches), p-Value (probability), FDR (false discovery rate; probability adjusted for multiple sampling), database (For the GO analysis: BP Biological process, CC Cellular Component, MF Molecular Function. For the pathway analysis: KEGG is Kyoto Encyclopedia of Genes and Genomes).
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