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Table 2 Gene Ontology terms enriched in genes with CNS specific AS and transcript levels

From: Functional coordination of alternative splicing in the mammalian central nervous system

GO term enrichment in genes with CNS tissue specific AS levels

Function/pathway

GO term

CNS count

CNS proportion

Total count

Total proportion

FDR

Signaling pathways

Cell-cell signaling

7

0.065

17

0.011

0.02820

 

Rho guanyl-nucleotide exchange factor activity

5

0.047

8

0.005

0.02820

 

Guanyl-nucleotide exchange factor activity

7

0.065

20

0.013

0.04400

 

Rho GTPase binding

3

0.028

3

0.002

0.04400

 

GTPase regulator activity

11

0.103

54

0.035

0.08280

Vesicular transport

Vesicle-mediated transport

13

0.121

64

0.042

0.04400

Cytoskeleton

Cytoskeletal protein binding

11

0.103

52

0.034

0.06720

 

Actin binding

8

0.075

32

0.021

0.09650

Nervous system

Transmission of nerve impulse

5

0.047

13

0.008

0.09770

 

Neurophysiologic process

6

0.056

20

0.013

0.10800

Other functions

Protein binding

49

0.458

449

0.291

0.03520

 

Plasma membrane

17

0.159

118

0.077

0.10800

GO term enrichment in genes with CNS tissue specific transcript levels

Signaling pathways

Cell-cell signaling

12

0.085

34

0.015

0.00022

 

Cell communication

35

0.246

334

0.143

0.03030

 

Insulin secretion

3

0.021

5

0.002

0.08710

 

Peptide hormone secretion

3

0.021

5

0.002

0.08710

 

Ionotropic glutamate receptor activity

2

0.014

2

0.001

0.09940

 

G-protein-coupled receptor binding

2

0.014

2

0.001

0.09940

 

Glutamate-gated ion channel activity

2

0.014

2

0.001

0.09940

 

Excitatory extracellular ligand-gated ion channel activity

3

0.021

6

0.003

0.09940

 

Cyclic-nucleotide-mediated signaling

3

0.021

7

0.003

0.13900

 

cAMP-mediated signaling

3

0.021

7

0.003

0.13900

 

G-protein coupled receptor protein signaling pathway

9

0.063

58

0.025

0.14800

Secretory pathways

Secretory pathway

10

0.070

45

0.019

0.02340

 

Secretion

10

0.070

51

0.022

0.04610

 

Regulated secretory pathway

4

0.028

11

0.005

0.09940

Cytoskeleton

Microtubule

8

0.056

40

0.017

0.08980

 

microtubule associated complex

5

0.035

19

0.008

0.10800

 

Cytoskeleton

16

0.113

136

0.058

0.14800

 

Microtubule-based process

7

0.049

39

0.017

0.14800

Nervous system

Transmission of nerve impulse

9

0.063

26

0.011

0.00456

 

Postsynaptic membrane

7

0.049

16

0.007

0.00512

 

Synaptic transmission

8

0.056

25

0.011

0.01100

 

Nervous system development

14

0.099

75

0.032

0.01500

 

Synaptosome

5

0.035

12

0.005

0.03030

 

Neurophysiologic process

9

0.063

43

0.018

0.04820

 

Neurogenesis

9

0.063

46

0.020

0.07040

 

Neurotransmitter secretion

4

0.028

10

0.004

0.08710

 

Neuron development

7

0.049

33

0.014

0.09940

 

Neuron differentiation

7

0.049

36

0.015

0.11400

 

Regulation of neurotransmitter levels

4

0.028

14

0.006

0.14800

Other functions

Membrane fraction

11

0.077

54

0.023

0.02340

 

System development

15

0.106

79

0.034

0.01020

 

Localization

44

0.310

487

0.209

0.09940

  1. Gene Ontology (GO) terms significantly enriched in the top approximately 100 genes with the most significant central nervous system (CNS) tissue specific alternative splicing (AS) levels, and the top approximately 200 genes with the most CNS specific transcript levels are shown. CNS counts (number of times a GO term appears in the CNS tissue regulated group) and total counts (number of times a GO term appears in the total group of microarray-profiled genes with sufficient expression across 15 tissues) are shown. Proportions in each group are also shown. FDR denotes the false discovery rate of a GO term. This value represents the expected proportion of false positive GO terms out of all positive GO terms. Only GO terms with a FDR below 0.15 are shown.
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Genome Biology

ISSN: 1474-760X

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