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Table 2 Pathways affected by the DMR-overlapping genes in the GBM0.2 tumours using the PANTHER Classification system

From: Modulation of mitochondrial DNA copy number in a model of glioblastoma induces changes to DNA methylation and gene expression of the nuclear genome in tumours

PANTHER pathways

Input/background

Fold enrichment

p value

FDR

PANTHER pathways

Input/background

Fold enrichment

p value

FDR

DMR-overlapping genes in the GBM0.2 tumours (p ≤ 0.001)

DMR-overlapping genes in the GBM0.2 tumours (adj. p ≤ 0.05)

 Cell differentiation (GO:0030154)

191/548

1.47

6.12E−06

9.95E−05

 Cell differentiation (GO:0030154)

9/459

3.93

5.42E−04

4.41E−02

 Nervous system development (GO:0007399)

113/314

1.52

1.88E−04

1.76E−03

 Nervous system Development (GO:0007399)

7/238

5.89

2.23E−04

5.45E−02

 Regulation of transcription from RNA polymerase II promoter (GO:0006357)

196/598

1.39

9.47E−05

9.63E−04

 Regulation of transcription from RNA polymerase II promoter (GO:0006357)

10/548

3.66

4.61E−04

5.63E−02

     

 Cellular process (GO:0009987)

57/7905

1.45

5.54E−04

2.70E−02

     

 Behaviour (GO:0007610)

4/76

10.55

6.79E−04

2.76E−02

 Developmental process (GO:0032502)

537/1501

1.51

1.01E−16

2.46E−14

     

 Sensory perception of smell (GO:0007608)

6/240

0.11

1.41E−15

1.72E−13

     

 Defence response to bacterium (GO:0042742)

0/112

< 0.01

9.10E−11

4.44E−09

     

 Response to biotic stimulus (GO:0009607)

3/144

0.09

2.98E−10

1.21E−08

     

 B cell mediated immunity (GO:0019724)

0/94

< 0.01

3.08E−09

9.40E−08

     

 Complement activation (GO:0006956)

1/94

0.04

5.91E−08

1.44E−06

     

 Ectoderm development (GO:0007398)

96/212

1.91

3.82E−07

8.46E−06

     

 Cell recognition (GO:0008037)

4/105

0.16

3.64E−06

6.84E−05

     

 Mesoderm development (GO:0007498)

109/269

1.71

4.74E−06

8.27E−05

     

 Phagocytosis (GO:0006909)

15/182

0.35

9.91E−06

1.42E−04

     

 Embryo development (GO:0009790)

49/106

1.95

1.96E−04

1.77E−03

     

 Cellular component morphogenesis (GO:0032989)

144/423

1.44

2.32E−04

2.02E−03

     

 Biological adhesion (GO:0022610)

124/356

1.47

2.72E−04

2.21E−03

     

 Cell adhesion (GO:0007155)

124/356

1.47

2.72E−04

2.29E−03

     

 Segment specification (GO:0007379)

37/78

2.01

7.86E−04

5.99E−03

     

 Transmembrane receptor protein tyrosine kinase signalling pathway (GO:0007169)

60/151

1.68

1.07E−03

7.90E−03

     

 Negative regulation of apoptotic process (GO:0043066)

43/99

1.84

1.25E−03

8.73E−03

     

 Regulation of phosphate metabolic process (GO:0019220)

169/537

1.33

1.34E−03

8.86E−03

     

 Intracellular signal transduction (GO:0035556)

310/1071

1.22

1.55E−03

9.92E−03

     

 Anterior/posterior axis specification (GO:0009948)

12/16

3.17

3.37E−03

1.96E−02

     

 Cytoskeleton organization (GO:0007010)

129/404

1.35

3.74E−03

2.12E−02

     

 Synaptic transmission (GO:0007268)

121/382

1.34

5.92E−03

3.28E−02

     
  1. Common processes are highlighted in italics