Copy Number

 

The putative cancer-causing HAMPs driven by SCNAs in each cancer type were identified by four criteria: 1) located in a peak region of a significantly recurrent focal SNCA locus estimated by the genomic identification of significant targets in cancer (GISTIC2) algorithm, (q≤0.25); 2) altered with high frequency and large amplitude (G-score ≥0.1); 3) mRNA reliably detected in at least 10% of tumor specimens in the given cancer type (90th percentile of FPKM value ≥1); and 4) mRNA significantly and positively correlated with copy numbers (Pearson P-value less than 0.001).

 

Summary of the G-score of the HAMPs in each cancer type


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HGNC Ensembl ACCBLCABRCACESCCHOLCOADDLBCESCAGBMHNSCKICHKIRCKIRPLAMLLGGLIHCLUADLUSCMESOOVPAADPCPGPRADREADSARCSKCMSTADTGCTTHCATHYMUCECUCSUVM
 Symbol  Gene ID  Amp  Del  Amp  Del  Amp  Del  Amp  Del  Amp  Del  Amp  Del  Amp  Del  Amp  Del  Amp  Del  Amp  Del  Amp  Del  Amp  Del  Amp  Del  Amp  Del  Amp  Del  Amp  Del  Amp  Del  Amp  Del  Amp  Del  Amp  Del  Amp  Del  Amp  Del  Amp  Del  Amp  Del  Amp  Del  Amp  Del  Amp  Del  Amp  Del  Amp  Del  Amp  Del  Amp  Del  Amp  Del  Amp  Del 
KAT6A  ENSG00000083168    0.09    0    0.27    0.05    0.44    0.05    0.1    0.02    0    0.02    0.18    0.02    0.03    0    0.43    0.06    0    0.01    0.14    0.03    0    0    0    0.01    0    0    0.01    0    0.01    0    0.07    0.05    0.2    0.03    0.45    0.03    0.02    0    0.39    0.05    0.03    0    0.01    0    0.03    0.11    0.18    0.03    0.15    0.07    0.05    0.02    0.09    0.04    0.02    0    0    0    0    0    0.26    0.01    0.99    0.07    0    0.01  
KAT6B  ENSG00000156650    0    0    0.11    0.03    0.19    0.03    0.01    0.01    0.25    0.01    0.04    0.02    0    0    0.08    0.03    0.01    0.03    0.04    0.03    0.03    0    0    0.01    0.01    0.01    0    0    0    0    0.03    0.04    0.04    0.02    0.08    0.04    0.01    0    0.32    0.1    0.06    0    0    0    0.01    0.07    0.12    0.04    0.05    0.13    0.01    0.01    0.19    0.05    0.01    0    0    0.01    0    0    0.26    0.03    0.65    0    0    0  
KAT7  ENSG00000136504    0.04    0.04    0.12    0.01    0.47    0.03    0.06    0    0.02    0.01    0.03    0.01    0    0    0.19    0.01    0.02    0.01    0.02    0.01    0    0    0    0    0.03    0    0    0    0.02    0.01    0.05    0.01    0.1    0    0.1    0.01    0.09    0    0.16    0.04    0.04    0.02    0.01    0.04    0.02    0.01    0.06    0.04    0.13    0.05    0.12    0.01    0.09    0.01    0.02    0    0    0    0    0    0.06    0.03    0.18    0.02    0.03    0.03  
KAT5  ENSG00000172977    0.07    0.07    0.2    0.01    0.14    0.09    0.13    0.01    0    0.11    0.01    0.02    0    0.02    0.18    0.04    0.01    0.03    0.3    0.02    0.07    0    0.01    0    0    0.01    0    0    0.01    0.01    0.02    0.04    0.09    0.03    0.09    0.02    0.08    0    0.23    0.04    0    0.03    0.03    0.01    0.08    0.01    0.02    0.04    0.13    0.03    0.08    0.06    0.07    0.03    0    0.04    0    0    0    0    0.07    0.03    0.2    0.06    0    0  
KAT8  ENSG00000103510    0    0    0.09    0.01    0.09    0.01    0.02    0.03    0    0.01    0.05    0    0.05    0    0.07    0    0    0.01    0.03    0.02    0    0    0    0    0.02    0    0    0.02    0.01    0.01    0.02    0    0.1    0.01    0.1    0.01    0    0    0.08    0.03    0    0    0    0    0    0.01    0.06    0    0.06    0.02    0.02    0.01    0.06    0    0.02    0.01    0    0    0    0    0.12    0    0.52    0.05    0    0  
CLOCK  ENSG00000134852    0.03    0    0.1    0.01    0.09    0.01    0.13    0.01    0    0.08    0.03    0.01    0    0.01    0.14    0.05    0.32    0.02    0.09    0.01    0.01    0    0.01    0    0    0    0    0    0.13    0.01    0.03    0.05    0.1    0.02    0.51    0.01    0    0.01    0.21    0.05    0.03    0.02    0.02    0.02    0.01    0.02    0.04    0.03    0.22    0.03    0.09    0.01    0.04    0.04    0.33    0    0    0    0    0    0.04    0    0.15    0.05    0    0  
HAT1  ENSG00000128708    0.02    0.01    0.07    0.04    0.06    0.03    0.09    0.01    0.05    0.01    0.01    0.01    0    0.06    0.23    0.01    0    0    0.13    0.01    0    0    0.02    0    0.06    0    0    0    0    0.01    0.06    0.06    0.05    0.01    0.13    0.02    0    0    0.37    0.03    0.03    0.02    0    0    0.01    0.09    0.03    0.02    0.03    0.1    0.03    0.02    0.04    0.03    0.04    0.01    0    0    0    0.01    0.06    0.01    0.16    0    0    0  
ELP3  ENSG00000134014    0.02    0    0.01    0.1    0.03    0.13    0    0.02    0    0.08    0.02    0.08    0    0.02    0.08    0.09    0.01    0.02    0.01    0.03    0    0.01    0    0.02    0    0    0    0    0    0    0.01    0.1    0.01    0.06    0    0.08    0    0.03    0.02    0.35    0    0.04    0.02    0.02    0.01    0.16    0    0.18    0.06    0.08    0.01    0.05    0.02    0.04    0.02    0    0    0    0    0    0.01    0.09    0.09    0.14    0    0.01  
KAT2A  ENSG00000108773    0.02    0.16    0.05    0.02    0.05    0.1    0.07    0.04    0.02    0.01    0.05    0.01    0.04    0    0.19    0.04    0.01    0.03    0.02    0.01    0    0    0    0    0    0    0    0.02    0    0.01    0.03    0.04    0.06    0.01    0.03    0.05    0.01    0.02    0.02    0.15    0.03    0.03    0.02    0.12    0    0.08    0.04    0.02    0.05    0.1    0.01    0.03    0.15    0.03    0.01    0.01    0    0    0    0    0.03    0.07    0    0.2    0    0.05  
KAT2B  ENSG00000114166    0.06    0.01    0.22    0.02    0.09    0.03    0.01    0.02    0.03    0.17    0.02    0.04    0    0.06    0.02    0.04    0    0.02    0.01    0.02    0.07    0    0    0.18    0    0.01    0    0.01    0.03    0.01    0.06    0.02    0.02    0.05    0.01    0.04    0.02    0.03    0.11    0.21    0.03    0.02    0    0.04    0.01    0.02    0.03    0.05    0.12    0.02    0.01    0.05    0.05    0.06    0.05    0.05    0    0    0    0.03    0.04    0.04    0.05    0.09    0    0  
TAF1  ENSG00000147133    0.01    0    0.05    0.02    0.02    0.02    0.04    0.02    0    0.01    0.01    0.01    0.03    0.02    0.1    0.03    0.01    0    0.04    0.01    0    0.01    0    0    0.01    0    0    0    0.03    0    0.02    0    0.03    0.02    0.05    0.04    0    0    0.14    0.03    0    0.01    0    0    0.01    0    0    0.02    0.18    0.07    0.02    0.01    0.03    0.02    0    0.01    0    0    0    0    0.04    0.01    0.18    0    0    0  
TAF1L  ENSG00000122728    0.12    0.07    0.07    0.04    0.04    0.03    0.01    0.01    0.19    0.01    0.01    0.01    0    0    0.18    0.04    0.03    0.1    0.11    0.04    0    0    0    0    0    0    0    0    0.01    0.02    0.01    0.02    0.07    0.03    0.29    0.05    0.01    0.11    0.07    0.09    0.04    0.01    0.01    0    0.01    0.02    0.01    0    0.07    0.04    0.06    0.07    0.11    0.04    0.02    0    0    0    0    0.02    0.04    0.02    0    0.05    0    0  
ATAT1  ENSG00000137343    0.01    0    0.17    0.02    0.1    0.02    0.2    0.02    0.08    0.03    0.03    0.01    0.05    0.04    0.19    0.04    0    0.01    0.05    0.04    0    0    0.01    0    0    0.01    0    0    0.01    0    0.14    0.01    0.1    0.01    0.07    0.04    0.02    0.02    0.32    0.05    0.03    0.01    0    0    0.01    0    0.07    0.01    0.04    0.06    0.13    0.01    0.13    0.04    0.01    0.01    0    0    0    0    0.06    0.01    0.21    0.03    0.13    0  
CREBBP  ENSG00000005339    0.12    0.02    0.01    0.22    0.09    0.04    0.12    0.02    0.05    0.05    0.03    0.03    0.05    0    0.01    0.07    0.02    0.02    0.03    0.03    0    0    0.01    0    0.01    0.01    0.02    0    0.01    0    0.02    0.03    0.05    0.04    0.03    0.11    0.04    0.02    0.1    0.29    0.02    0.02    0    0.01    0.01    0    0.02    0.03    0.08    0.03    0.07    0.02    0.03    0.09    0    0    0    0    0    0    0.04    0.08    0    0.1    0    0  
EP300  ENSG00000100393    0.04    0    0.01    0.12    0.03    0.03    0.04    0.07    0.04    0.01    0.01    0.02    0    0    0.03    0    0.01    0.05    0.03    0.01    0    0    0    0    0.01    0.01    0    0    0    0.03    0.03    0.02    0.04    0.03    0.06    0.02    0    0.04    0.02    0.25    0.05    0.03    0    0.06    0    0.01    0.01    0.05    0.08    0.05    0.33    0    0.02    0.01    0    0.03    0    0    0    0.03    0.05    0.05    0.17    0.15    0    0  
GTF3C4  ENSG00000125484    0.1    0.04    0.04    0.03    0.04    0.05    0.07    0.01    0.06    0.01    0.02    0.01    0.05    0    0.12    0.04    0.03    0.04    0.07    0.03    0    0    0    0.01    0.01    0.01    0.01    0    0.02    0.01    0.04    0.03    0.04    0.03    0.08    0.02    0    0.04    0.06    0.25    0    0    0    0.01    0.02    0.01    0.05    0.04    0.04    0.15    0.02    0.03    0.11    0.01    0.03    0.03    0    0    0    0.01    0.02    0.06    0.03    0.14    0    0  
NCOA1  ENSG00000084676    0.03    0.04    0.1    0.01    0.05    0.04    0.08    0    0    0.05    0.01    0.01    0.02    0.03    0.06    0.06    0.02    0.04    0.03    0.02    0    0    0    0    0.02    0.01    0    0.01    0.01    0.01    0.09    0.01    0.05    0.01    0.09    0.02    0.03    0.08    0.19    0.12    0.01    0.04    0.01    0    0.02    0.01    0.01    0.02    0.05    0.11    0.05    0.04    0.03    0.04    0.17    0.01    0    0    0    0    0.1    0.02    0.33    0.03    0.05    0  
NCOA3  ENSG00000124151    0.01    0    0.11    0.01    0.17    0.02    0.01    0.04    0    0.01    0.12    0    0    0    0.05    0    0.02    0.01    0.01    0.01    0    0    0.01    0    0    0    0    0.03    0    0    0.04    0.01    0.09    0.04    0.09    0.03    0.02    0    0.39    0.02    0    0    0    0.01    0.04    0.01    0.12    0    0.13    0.04    0.06    0    0.21    0.01    0.01    0.01    0    0    0    0    0.17    0.01    0.46    0    0    0  
SP140  ENSG00000079263    0.03    0.05    0    0.31    0.02    0.09    0.01    0.36    0    0.04    0.02    0.03    0    0    0.04    0.15    0    0.01    0.01    0.18    0    0.05    0.01    0.07    0.04    0.04    0    0    0.01    0.06    0.03    0.05    0.03    0.04    0.02    0.2    0    0.07    0.14    0.2    0.07    0.01    0    0.01    0.01    0.03    0.02    0.02    0.04    0.34    0.02    0.08    0.04    0.04    0.05    0.03    0    0.01    0    0.03    0.03    0.05    0.13    0.06    0.04    0.05  
SP140L  ENSG00000185404    0.03    0.05    0    0.31    0.02    0.09    0.01    0.36    0    0.01    0.02    0.03    0    0    0.04    0.15    0    0.01    0.01    0.18    0    0.05    0.01    0.07    0.04    0.04    0    0    0.01    0.06    0.03    0.05    0.03    0.04    0.02    0.2    0    0.07    0.14    0.2    0.07    0.01    0    0.01    0.01    0.03    0.02    0.02    0.03    0.34    0.02    0.08    0.04    0.05    0.05    0.03    0    0.01    0    0.03    0.03    0.05    0.13    0.06    0.04    0.05  

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