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. 2017 Sep 8;8(44):77649–77672. doi: 10.18632/oncotarget.20765

Table 3. Network that includes the 8 query genes (E2F1, E2F2, E2F3, BUBR1, TTK, NDC80, Nek2, Sgo1) and the 50 most frequently altered neighbor genes (out of 279).

Gene Function Total Alterations Amplification Homozygous Deletion Up-regulation Down-regulation Mutation
AHCTF1 Putative AT-hook-containing transcription factor 36.5% 14.6% 0.1% 29.6% 0.4% 1.6%
AURKA Microtubule formation and/or stabilization, centrosome homeostasis 20.4% 5.6% 0.0% 18.6% 0.0% 0.5%
BIRC5 Inhibitor of apoptosis (IAP) gene family 15.3% 6.2% 0.1% 12.9% 0.0% 0.0%
BRCA1 DNA repair, centrosome amplification, chromosome instability 13.5% 1.8% 0.8% 9.7% 0.0% 2.5%
BUBR1 Spindle checkpoint 8.7% 0.4% 1.1% 7.0% 0.0% 0.3%
CP110 Centriolar protein 16.5% 4.3% 0.0% 13.6% 0.0% 0.4%
CDC16 Ubiquitin ligase, component of the APC complex 24.6% 2.5% 0.7% 9.1% 14.9% 0.3%
CDC6 Early DNA replication 15.3% 6.5% 0.3% 13.3% 0.0% 0.3%
CENPF Centromere-kinetochore, spindle, midzone 25.5% 12.5% 0.0% 15.6% 0.0% 1.3%
CENPL Kinetochore, mitotic progression 28.1% 10.0% 0.0% 22.0% 0.0% 0.5%
CEP250 Centriole-centriole cohesion 18.4% 2.8% 0.1% 15.0% 1.3% 1.2%
CREBBP Histone acetyl-transferase, transcriptional co-activation 20.8% 5.1% 0.4% 14.0% 1.9% 2.0%
CSNK1D DNA replication and repair, apoptosis, microtubule dynamics, chromosome segregation 16.8% 6.2% 0.6% 10.1% 3.4% 0.1%
DSN1 Kinetochore assembly and progression through the cell cycle 15.9% 2.0% 0.0% 15.0% 0.0% 0.4%
E2F1 Cell cycle, centrosome amplification 10.6% 1.2% 0.1% 9.3% 0.0% 0.6%
E2F2 Cell cycle, centrosome amplification 4.9% 0.0% 0.4% 4.5% 0.0% 0.0%
E2F3 Cell cycle, centrosome amplification 13.7% 2.3% 0.2% 12.8% 0.0% 0.2%
FOXM1 Cell proliferation 15.2% 2.8% 0.1% 14.5% 0.0% 0.6%
KLHL12 May act as a substrate adaptor of the Cullin-3 ubiquitin ligase complex 35.2% 12.9% 0.0% 29.7% 0.4% 0.3%
LRRC59 Ribosome binding protein 20.2% 7.8% 0.1% 19.4% 0.0% 0.1%
MAPRE1 Microtubules, dynactin complex, mitotic centrosomes and spindle microtubules 19.1% 1.5% 0.1% 18.3% 0.4% 0.1%
MCL1 Anti-apoptotic protein 19.3% 14.4% 0.0% 9.7% 0.0% 0.1%
MDM4 Binds and inhibits p53, suppresses MDM2 function 26.4% 13.9% 0.0% 18.3% 0.0% 0.3%
MYC Cell cycle progression, apoptosis 26.2% 21.9% 0.0% 6.7% 0.0% 0.3%
NCOA3 Histone acetyltransferase, transcriptional co-activator 21.2% 3.8% 0.0% 16.4% 0.3% 4.7%
NCOA6 Transcriptional co-activator 17.9% 2.0% 0.0% 14.7% 1.5% 1.8%
NDC80 (Hec-1) Chromosome segregation 10.3% 10.3% 0.5% 9.5% 0.0% 0.4%
NDE1 Microtubule organization, mitosis and neuronal migration 14.7% 4.5% 0.0% 11.4% 0.2% 0.2%
NEK2 Centrosome separation, mitotic checkpoint 29.6% 12.3% 0.0% 21.7% 0.0% 0.1%
NSL1 Kinetochores 39.4% 12.0% 0.0% 34.6% 1.0% 0.5%
NUF2 Centromere 26.6% 12.4% 0.0% 19.8% 0.0% 0.3%
NUP107 Nuclear pore complex 13.3% 3.3% 0.0% 11.3% 0.4% 0.9%
NUP133 Nuclear envelope, kinetochores 38.9% 13.7% 0.0% 33.6% 1.0% 0.3%
NUP85 Nuclear pore complex 19.6% 6.2% 0.0% 17.7% 0.1% 0.1%
PARP1 DNA damage response 37.3% 13.6% 0.0% 29.9% 0.1% 0.9%
PHB Cellular senescence 16.4% 8.1% 0.1% 14.5% 0.0%
PMF1 25.5% 11.3% 0.0% 18.1% 0.0% 0.0%
PPP2CB Phosphatase, negative control of cell cycle 24.0% 1.8% 4.7% 5.6% 15.9% 0.3%
PPP2R5A Phosphatase, negative control of cell cycle 22.6% 12.0% 0.0% 14.7% 0.0% 0.1%
PPP2R5D Phosphatase involved in negative control of cell cycle 17.8% 2.1% 0.3% 15.1% 2.2% 0.4%
PRKDC DNA double strand break repair and recombination 24.1% 6.8% 0.1% 18.6% 0.0% 2.1%
RB1 Regulator of the cell cycle, centrosome amplification 14.7% 0.2% 4.5% 2.9% 7.6% 2.3%
RBL1 (p107) Negative regulator of the cell cycle 13.9% 2.1% 0.1% 12.4% 0.0% 0.8%
RPL7 Ribosomal protein 23.2% 10.4% 0.1% 18.1% 0.0% 0.1%
RPS27 Ribosomal protein 19.2% 12.2% 0.0% 8.9% 0.0% 0.0%
RPS6KB1 Protein synthesis, cell growth, and cell proliferation 25.0% 11.0% 0.0% 22.5% 1.2% 0.4%
SDCCAG8 Organizing the centrosome 33.6% 14.5% 0.0% 24.9% 1.2% 0.7%
SGO1 Protects centromeric cohesin from cleavage 10.3% 1.2% 0.1% 9.7% 0.0% 0.2%
SKA2 Spindle and kinetochore 21.2% 9.0% 0.1% 18.7% 0.0% 0.0%
SKP2 Ubiquitination, degradation of p27KIP1 13.2% 2.0% 0.3% 11.9% 0.0% 0.2%
TFDP1 Binds E2Fs and enhances their DNA binding 13.5% 2.6% 0.5% 11.2% 1.1% 0.5%
TK1 Thymidine kinase 14.4% 6.2% 0.1% 11.3% 0.0% 0.1%
TOM1L1 Src activating and signaling molecule 14.4% 7.2% 0.0% 12.3% 0.4% 0.3%
TP53 Cell cycle arrest, apoptosis, senescence, DNA repair, centrosome amplification 38.0% 0.1% 1.3% 5.0% 3.4% 35.0%
Mps1/TTK Centrosome duplication, spindle assembly checkpoint 7.4% 0.2% 0.2% 6.8% 0.0% 0.4%
TUBGCP3 Tubulin gamma complex-associated protein 16.0% 2.6% 0.4% 10.0% 4.8% 0.5%
UBE2C E2 ubiquitin-conjugating enzyme family, cell cycle progression 13.2% 3.2% 0.1% 11.2% 0.0% 0.0%
XRCC6 Repair of non-homologous DNA ends 16.8% 0.3% 0.1% 7.1% 9.1% 0.6%