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 
SP100  ENSG00000067066    0.03    0.06    0    0.31    0.02    0.09    0.02    0.36    0    0.01    0.02    0.03    0    0    0.04    0.16    0    0.01    0.01    0.19    0    0.05    0.01    0.07    0.04    0.04    0    0    0    0.07    0.03    0.05    0.04    0.04    0.02    0.2    0    0.07    0.15    0.19    0.07    0.01    0    0.01    0.01    0.02    0.02    0.02    0.03    0.35    0.01    0.09    0.03    0.05    0.05    0.03    0    0.01    0    0.03    0.03    0.05    0.13    0.06    0.04    0.05  
SP110  ENSG00000135899    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    0.19    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    0.01    0.08    0.03    0.04    0.05    0.03    0    0.01    0    0.03    0.03    0.05    0.13    0.06    0.04    0.05  
TRIM28  ENSG00000130726    0.14    0.01    0.15    0.04    0.15    0.06    0.12    0.05    0.02    0.07    0.02    0.03    0.16    0.03    0.25    0.06    0.05    0.12    0.07    0.05    0    0    0.01    0    0    0.02    0.02    0.01    0.01    0.17    0.07    0.03    0.04    0.07    0.13    0.09    0.03    0.04    0.18    0.35    0.05    0.04    0    0.03    0.01    0    0.02    0.04    0.07    0.3    0.04    0.06    0.15    0.03    0    0.06    0    0    0    0    0.08    0.07    0.14    0.12    0    0  
TRIM33  ENSG00000197323    0.02    0.05    0.07    0.05    0.06    0.08    0.01    0.08    0    0.15    0    0.07    0.03    0.05    0.09    0.19    0.01    0.03    0    0.15    0    0    0    0    0    0.01    0    0.01    0    0.01    0    0.03    0.01    0.14    0.02    0.17    0    0.33    0.16    0.14    0.01    0.02    0.03    0.26    0    0.04    0.06    0.08    0.03    0.12    0.13    0.1    0.04    0.08    0.05    0.03    0    0    0    0    0.02    0.03    0.06    0.06    0    0.05  
TRIM24  ENSG00000122779    0.03    0.06    0.04    0.03    0.09    0.04    0.04    0.08    0    0.02    0.03    0    0.02    0.09    0.04    0.18    0.05    0.01    0.03    0.14    0.06    0    0.01    0.01    0.09    0    0    0.05    0.11    0.01    0.05    0.04    0.09    0.02    0.08    0.07    0.04    0.05    0.5    0.04    0.01    0.05    0.01    0.01    0.02    0.02    0.03    0.01    0.12    0.08    0.21    0.02    0.03    0.07    0.02    0.04    0    0    0    0.01    0.05    0.05    0.08    0.14    0    0  
TRIM66  ENSG00000166436    0.01    0.04    0    0.1    0.04    0.09    0.01    0.05    0.03    0.01    0.03    0    0.02    0    0.06    0.07    0.02    0.04    0.01    0.06    0    0.03    0    0    0    0    0    0    0.01    0.08    0.03    0.02    0.01    0.05    0.01    0.13    0.02    0.07    0.01    0.39    0    0.04    0.03    0.07    0.01    0.01    0.01    0.01    0.07    0.12    0.01    0.02    0.02    0.04    0.03    0    0    0    0    0    0.02    0.07    0.13    0.05    0    0  
BAZ1A  ENSG00000198604    0.11    0.03    0.04    0.06    0.16    0.02    0.07    0    0.05    0.02    0.03    0.01    0    0    0.17    0.03    0.01    0.08    0.07    0.03    0    0    0.02    0    0.01    0    0    0    0.01    0.01    0.06    0.04    0.6    0.01    0.13    0.05    0    0.02    0.15    0.11    0.01    0.01    0    0.02    0.02    0.01    0.02    0.03    0.22    0.05    0.02    0.01    0.08    0.02    0.03    0    0    0    0    0.01    0.05    0.02    0.1    0.03    0    0  
SMARCA2  ENSG00000080503    0.09    0.03    0.13    0.08    0.11    0.06    0.14    0.05    0.03    0.01    0.02    0.02    0.08    0.02    0.07    0.17    0.01    0.17    0.17    0.08    0    0.03    0.02    0    0    0.02    0    0    0.01    0.09    0.06    0.04    0.04    0.12    0.13    0.11    0.04    0.06    0.21    0.19    0.01    0.07    0.01    0.04    0.01    0.06    0.04    0.05    0.16    0.16    0.05    0.1    0.12    0.12    0.01    0.1    0    0    0.01    0.01    0.08    0.03    0    0.19    0    0  
SMARCA4  ENSG00000127616    0.14    0.02    0.09    0.05    0.09    0.05    0.13    0.05    0    0.01    0.02    0.02    0    0.03    0.12    0.11    0.06    0.01    0.06    0.03    0    0    0    0    0    0.02    0.03    0    0.01    0    0.05    0.11    0.02    0.09    0.09    0.07    0.09    0.01    0.58    0.2    0.01    0.07    0    0    0.01    0.02    0.03    0.02    0.31    0.02    0.02    0.03    0.07    0.06    0.02    0    0    0.01    0    0.01    0.26    0.04    0.65    0.13    0.07    0.02  
ASH1L  ENSG00000116539    0.16    0.02    0.36    0.01    0.34    0.01    0.19    0.01    0.58    0.01    0.03    0    0.25    0    0.2    0    0.07    0    0.05    0.01    0    0.03    0.03    0    0.01    0    0    0    0.02    0    0.37    0    0.37    0    0.26    0    0.11    0    0.57    0.02    0.09    0    0.06    0    0.05    0.03    0.11    0    0.41    0.01    0.21    0    0.16    0.01    0.09    0    0    0    0.02    0    0.23    0    0.96    0.01    0    0  
BAZ1B  ENSG00000009954    0.15    0    0.05    0.02    0.09    0.02    0.04    0.01    0    0.01    0.01    0    0.1    0    0.17    0.03    0.05    0    0.04    0.03    0    0    0.01    0    0.03    0    0    0    0.01    0.01    0.08    0.01    0.02    0.02    0.1    0.02    0.02    0    0.17    0.06    0.02    0    0    0.02    0.03    0    0.01    0    0.07    0.03    0.06    0.02    0.09    0.02    0.12    0    0    0    0    0    0.06    0.02    0.12    0    0    0  
PBRM1  ENSG00000163939    0.15    0.01    0.04    0.16    0.01    0.17    0    0.07    0    0.2    0    0.06    0    0.06    0.03    0.13    0.02    0.05    0    0.06    0    0.02    0    0.18    0    0.03    0    0.01    0.01    0.06    0.03    0.08    0.02    0.06    0.01    0.11    0    0.64    0.08    0.22    0    0.05    0    0.04    0    0.03    0.02    0.07    0.04    0.15    0.02    0.04    0.02    0.13    0.05    0.01    0    0    0    0.03    0.08    0.07    0.05    0.3    0    0.03  
ZMYND8  ENSG00000101040    0.08    0    0.11    0.01    0.18    0.02    0.02    0.04    0.05    0.01    0.13    0    0    0    0.07    0    0.01    0.01    0.01    0.01    0    0    0.01    0    0    0    0    0.03    0.01    0.01    0.05    0.01    0.1    0.04    0.09    0.01    0    0    0.44    0.03    0    0    0.02    0.01    0.04    0.01    0.14    0    0.13    0.04    0.06    0    0.17    0.01    0    0.01    0    0    0    0    0.19    0.01    0.4    0    0    0  
ZMYND11  ENSG00000015171    0    0.03    0.24    0.02    0.16    0.03    0.04    0.03    0    0.05    0.02    0.04    0.07    0.09    0.07    0.12    0.02    0.06    0.03    0.06    0    0.04    0.01    0.02    0.03    0.02    0.01    0.02    0.08    0.02    0.03    0.03    0.06    0.09    0.03    0.13    0.02    0.17    0.34    0.18    0.01    0.05    0.01    0.01    0.01    0.03    0.02    0.03    0.09    0.35    0.03    0.1    0.06    0.06    0.01    0.07    0    0    0    0    0.07    0.03    0.32    0    0    0.02  
BRD4  ENSG00000141867    0.35    0    0.03    0.05    0.15    0.03    0.02    0.07    0    0.03    0.02    0.01    0    0.02    0.23    0.06    0.03    0    0.07    0.02    0    0    0    0    0    0    0.01    0    0.02    0    0.14    0.04    0.01    0.02    0.13    0.04    0.06    0    0.92    0.08    0.01    0    0    0    0.01    0    0.03    0.01    0.16    0.02    0.04    0.01    0.06    0.03    0    0    0    0    0    0    0.28    0.03    0.5    0.05    0.02    0  
BPTF  ENSG00000171634    0.17    0.06    0.2    0.01    0.57    0.01    0.15    0.02    0.12    0.01    0.12    0.01    0.05    0    0.22    0.03    0.03    0.01    0.07    0.02    0.02    0    0.02    0    0.04    0    0.01    0    0.06    0    0.21    0.01    0.16    0    0.21    0    0.12    0    0.25    0.03    0.07    0.1    0.02    0.01    0.03    0.02    0.09    0.01    0.21    0.04    0.24    0.01    0.1    0.03    0.04    0    0    0    0.02    0    0.15    0.01    0.49    0.02    0.17    0.01  
BRD2  ENSG00000204256    0.03    0    0.08    0.04    0.08    0.02    0.09    0.01    0.05    0.03    0.03    0.02    0.02    0.2    0.15    0.04    0.01    0.01    0.02    0.04    0    0    0    0    0    0.02    0    0    0.01    0    0.08    0.01    0.07    0.01    0.04    0.05    0.02    0.02    0.28    0.06    0.03    0.01    0    0    0.01    0    0.06    0.02    0.05    0.07    0.11    0.01    0.07    0.04    0    0.01    0    0    0    0    0.05    0.01    0.05    0.01    0.11    0  
BRDT  ENSG00000137948    0.02    0.05    0.05    0.07    0.05    0.11    0    0.05    0    0.1    0    0.07    0    0.03    0    0.08    0.01    0.06    0.01    0.08    0    0    0    0.01    0    0.01    0.01    0    0.01    0.01    0.01    0.03    0.05    0.09    0.05    0.06    0    0.39    0.16    0.17    0    0.02    0    0.23    0.01    0.07    0.01    0.05    0.08    0.08    0.03    0.12    0.01    0.07    0.04    0.06    0    0    0    0    0.02    0.03    0.05    0.06    0    0.05  
BRD3  ENSG00000169925    0.12    0.04    0.04    0.03    0.05    0.06    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    0.08    0.03    0.05    0.03    0.08    0.02    0.05    0.02    0.07    0.25    0.01    0    0.02    0.01    0.03    0.01    0.05    0.03    0.05    0.15    0.03    0.02    0.12    0.01    0.03    0.06    0    0    0    0.01    0.01    0.06    0.03    0.14    0    0  
KMT2A  ENSG00000118058    0.07    0.05    0.04    0.11    0.03    0.22    0.04    0.3    0    0.17    0.01    0.01    0.14    0.01    0.04    0.12    0.03    0.01    0.05    0.16    0.02    0.02    0.02    0.01    0    0.06    0.19    0.03    0.07    0.01    0.01    0.09    0.06    0.08    0.05    0.09    0.09    0.04    0.18    0.14    0.01    0.02    0    0.06    0.02    0.08    0.03    0.03    0.03    0.23    0    0.26    0.09    0.07    0    0.15    0    0    0    0.02    0.06    0.04    0.32    0.16    0    0.07  

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