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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
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Epigenetics & Chromatin

ISSN: 1756-8935