Table 4. Biological processes overrepresented among the correlating genes within recurrent and predictive regions.
| GO number | GO category | No. correlating genes | No. genes on the array | p-value | Correlating genes |
| Gains | |||||
| GO: 000815 | Biological process | 93a | 5824a | ||
| GO: 0006915 | Apoptosis | 13 (14.0%) | 434 (7.5%) | 0.026 | UBE4B, BIRC2, BIRC3 , ATF5, BCAP31, CLPTM1L, DAP, FASTKD3, FXR1, NUP62, PAK2, PDCD10, SLC25A6 |
| GO: 0005975 | Carbohydrate metabolism | 7 (7.5%) | 198 (3.4%) | 0.038 | PPP1R2, ARNT, PHKA2, POFUT1, PDHA1, TSTA3, IDH3G |
| GO: 0006412 | Translation | 7 (7.5%) | 163 (2.8%) | 0.015 | EIF4G1, EIF4A2, EIF2S2, MRPS12, RPS16, EIF2S3, MRPS2 |
| GO: 0022613 | RNA-protein complex biogenesis and assembly | 7 (7.5%) | 89 (1.5%) | 0.001 | EIF4G1, EIF4A2, EIF2S2, EIF2S3, EBNA1BP2, NCBP2, RCL1 |
| Losses | |||||
| GO: 000815 | Biological process | 62a | 5824a | ||
| GO: 0033036 | Macromolecule localization | 10 (16.1%) | 427 (7.3%) | 0.022 | BIN3, COPB1, COG6, XPO7, HRB, MYO6, PDIA4, SNX19, TIMM8B, TSG101 |
| GO: 0006091 | Generation of precursor metabolites and energy | 4 (6.5%) | 117 (2.0%) | 0.035 | ATP5J, COX7C, GBE1, NDUFS1 |
| GO: 0006366 | Transcription from RNA polymerase II promoter | 10 (16.1%) | 357 (6.1) | 0.004 | RYBP, FOXO3, GTF2F2, GTF2H1, MED4, MYO6, POU2F3, SMARCAL1, ZNF202, HDAC4 |
| GO: 0006325 | Establishment or maintenance of chromatin architecture | 5 (8.1%) | 140 (2.4%) | 0.016 | DSE, H2AFX, HDAC2, SMARCAL1, HDAC4 |
a
Genes with GO annotation (biological process).