Table 2.
Pathways affected by the DMR-overlapping genes in the GBM0.2 tumours using the PANTHER Classification system
| 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 | |||||
Common processes are highlighted in italics