Copy Number

 

The putative cancer-associated PDGs 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 PDGs in each cancer type


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KIRCKIRPKICHPRADBLCATHYMMESOLUADLUSCHNSCESCASTADCOADREADPAADLIHCCHOLACCPCPGTHCABRCAOVCESCUCECUCSSARCTGCTLAMLDLBCLGGGBMUVMSKCM
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PECRENSG00000115425  0.02    0.07    0.04    0.03    0.00    0.03    0.01    0.03    0.01    0.26    0.00    0.00    0.00    0.12    0.03    0.03    0.04    0.19    0.00    0.18    0.03    0.13    0.05    0.05    0.02    0.02    0.02    0.02    0.06    0.03    0.03    0.04    0.00    0.01    0.03    0.03    0.00    0.00    0.00    0.01    0.04    0.06    0.20    0.17    0.03    0.33    0.03    0.04    0.08    0.05    0.05    0.21    0.08    0.02    0.00    0.00    0.00    0.04    0.00    0.02    0.00    0.00    0.02    0.02    0.02    0.04  
CHD9ENSG00000177200  0.00    0.01    0.01    0.01    0.00    0.00    0.01    0.07    0.05    0.05    0.00    0.00    0.00    0.04    0.07    0.03    0.05    0.02    0.02    0.04    0.10    0.01    0.02    0.04    0.04    0.00    0.02    0.00    0.01    0.00    0.02    0.04    0.00    0.04    0.09    0.05    0.01    0.03    0.00    0.00    0.09    0.05    0.05    0.16    0.00    0.08    0.03    0.06    0.05    0.19    0.03    0.14    0.10    0.01    0.01    0.00    0.00    0.04    0.00    0.01    0.00    0.04    0.00    0.03    0.00    0.05  
TULP3ENSG00000078246  0.02    0.00    0.01    0.01    0.02    0.00    0.02    0.06    0.11    0.03    0.01    0.00    0.02    0.01    0.07    0.07    0.21    0.01    0.15    0.01    0.13    0.03    0.10    0.06    0.15    0.01    0.12    0.02    0.12    0.03    0.04    0.04    0.19    0.05    0.03    0.00    0.00    0.01    0.00    0.00    0.13    0.04    0.47    0.07    0.05    0.02    0.10    0.02    0.22    0.14    0.14    0.13    0.57    0.00    0.00    0.01    0.02    0.03    0.15    0.01    0.07    0.02    0.00    0.01    0.06    0.02  
MAST1ENSG00000105613  0.00    0.00    0.01    0.01    0.00    0.00    0.00    0.02    0.05    0.05    0.01    0.00    0.09    0.01    0.01    0.05    0.09    0.05    0.06    0.03    0.10    0.05    0.03    0.03    0.00    0.01    0.01    0.02    0.01    0.02    0.02    0.09    0.00    0.01    0.17    0.00    0.00    0.00    0.00    0.01    0.08    0.04    0.71    0.13    0.14    0.04    0.22    0.04    0.27    0.14    0.18    0.03    0.02    0.00    0.01    0.00    0.00    0.00    0.01    0.01    0.04    0.00    0.02    0.00    0.02    0.02  
PRKAG2ENSG00000106617  0.03    0.01    0.04    0.00    0.05    0.02    0.03    0.04    0.05    0.06    0.00    0.01    0.00    0.04    0.12    0.02    0.09    0.10    0.02    0.17    0.05    0.25    0.03    0.10    0.02    0.01    0.01    0.03    0.02    0.06    0.07    0.04    0.00    0.06    0.13    0.05    0.00    0.03    0.00    0.00    0.07    0.08    0.56    0.09    0.04    0.10    0.05    0.06    0.17    0.23    0.09    0.15    0.01    0.05    0.00    0.06    0.02    0.09    0.10    0.00    0.09    0.01    0.00    0.03    0.20    0.03  
TAF3ENSG00000165632  0.01    0.01    0.03    0.00    0.00    0.00    0.02    0.03    0.51    0.01    0.00    0.00    0.02    0.11    0.03    0.05    0.03    0.07    0.02    0.03    0.10    0.05    0.07    0.05    0.01    0.02    0.02    0.00    0.03    0.02    0.01    0.01    0.00    0.05    0.07    0.06    0.02    0.00    0.00    0.01    0.17    0.01    0.27    0.11    0.03    0.02    0.03    0.01    0.15    0.00    0.04    0.07    0.00    0.02    0.00    0.00    0.04    0.02    0.05    0.01    0.02    0.01    0.00    0.02    0.02    0.02  
YES1ENSG00000176105  0.00    0.00    0.01    0.00    0.01    0.01    0.01    0.03    0.08    0.02    0.00    0.00    0.00    0.00    0.06    0.02    0.18    0.04    0.18    0.03    0.30    0.06    0.07    0.02    0.02    0.01    0.02    0.05    0.03    0.03    0.02    0.02    0.00    0.05    0.00    0.06    0.00    0.00    0.00    0.00    0.04    0.04    0.15    0.11    0.06    0.03    0.06    0.03    0.10    0.07    0.12    0.12    0.00    0.11    0.00    0.01    0.03    0.04    0.02    0.03    0.01    0.04    0.00    0.00    0.05    0.02  
ZMPSTE24ENSG00000084073  0.01    0.02    0.01    0.03    0.00    0.00    0.01    0.01    0.31    0.02    0.00    0.00    0.11    0.03    0.13    0.02    0.14    0.02    0.08    0.02    0.31    0.02    0.07    0.03    0.04    0.02    0.02    0.03    0.04    0.01    0.03    0.10    0.00    0.26    0.00    0.03    0.03    0.07    0.00    0.00    0.08    0.05    0.73    0.05    0.07    0.01    0.14    0.01    0.22    0.05    0.11    0.04    0.04    0.03    0.02    0.00    0.00    0.03    0.00    0.01    0.03    0.02    0.00    0.10    0.05    0.02  
KCNMA1ENSG00000156113  0.00    0.01    0.00    0.00    0.03    0.00    0.00    0.05    0.11    0.02    0.00    0.00    0.01    0.00    0.05    0.02    0.07    0.05    0.04    0.04    0.06    0.04    0.16    0.03    0.04    0.04    0.15    0.02    0.06    0.00    0.04    0.04    0.25    0.01    0.05    0.03    0.01    0.00    0.00    0.02    0.14    0.04    0.37    0.11    0.03    0.02    0.21    0.04    0.51    0.06    0.10    0.13    0.01    0.01    0.00    0.00    0.00    0.05    0.00    0.01    0.01    0.03    0.00    0.00    0.00    0.02  
CACNA1EENSG00000198216  0.02    0.00    0.00    0.01    0.00    0.00    0.01    0.03    0.21    0.02    0.02    0.00    0.10    0.03    0.10    0.00    0.15    0.01    0.03    0.00    0.15    0.02    0.09    0.01    0.03    0.00    0.12    0.00    0.04    0.01    0.18    0.01    0.17    0.01    0.02    0.04    0.02    0.00    0.01    0.00    0.17    0.01    0.36    0.03    0.08    0.01    0.07    0.00    0.29    0.00    0.26    0.03    0.07    0.00    0.01    0.00    0.32    0.02    0.01    0.00    0.02    0.01    0.02    0.00    0.12    0.02  
CACNA1BENSG00000148408  0.01    0.01    0.01    0.01    0.00    0.08    0.02    0.01    0.05    0.03    0.00    0.00    0.00    0.02    0.08    0.04    0.08    0.03    0.10    0.05    0.18    0.01    0.14    0.02    0.04    0.01    0.11    0.04    0.02    0.00    0.05    0.04    0.07    0.01    0.12    0.03    0.00    0.02    0.01    0.00    0.05    0.07    0.19    0.22    0.08    0.03    0.03    0.04    0.02    0.14    0.09    0.19    0.03    0.04    0.03    0.00    0.05    0.00    0.04    0.01    0.05    0.02    0.00    0.00    0.04    0.03  
CDH13ENSG00000140945  0.01    0.01    0.00    0.04    0.00    0.08    0.01    0.25    0.10    0.05    0.00    0.01    0.01    0.19    0.02    0.10    0.05    0.08    0.04    0.11    0.06    0.10    0.03    0.05    0.02    0.05    0.02    0.05    0.01    0.02    0.00    0.06    0.05    0.01    0.06    0.08    0.01    0.02    0.00    0.01    0.04    0.08    0.05    0.34    0.04    0.07    0.01    0.08    0.01    0.24    0.08    0.07    0.00    0.11    0.00    0.04    0.03    0.06    0.00    0.02    0.01    0.04    0.00    0.07    0.02    0.09  
TMPRSS11EENSG00000087128  0.01    0.00    0.01    0.00    0.00    0.00    0.02    0.04    0.11    0.03    0.00    0.00    0.00    0.06    0.05    0.03    0.21    0.01    0.08    0.02    0.13    0.01    0.03    0.02    0.01    0.01    0.03    0.01    0.00    0.01    0.01    0.06    0.00    0.03    0.03    0.00    0.04    0.02    0.00    0.00    0.08    0.02    0.20    0.08    0.04    0.04    0.04    0.01    0.02    0.05    0.06    0.06    0.09    0.01    0.00    0.01    0.00    0.03    0.00    0.02    0.00    0.02    0.00    0.00    0.02    0.04  
NEK6ENSG00000119408  0.00    0.00    0.01    0.00    0.00    0.00    0.03    0.01    0.02    0.03    0.00    0.01    0.00    0.02    0.04    0.02    0.05    0.03    0.07    0.01    0.10    0.02    0.09    0.02    0.01    0.01    0.04    0.02    0.00    0.01    0.03    0.04    0.06    0.04    0.08    0.05    0.01    0.00    0.00    0.00    0.07    0.03    0.12    0.14    0.02    0.01    0.02    0.04    0.05    0.16    0.12    0.04    0.02    0.02    0.01    0.00    0.05    0.05    0.02    0.00    0.04    0.02    0.00    0.00    0.02    0.03  
CHD1ENSG00000153922  0.08    0.01    0.02    0.01    0.00    0.01    0.01    0.27    0.02    0.08    0.00    0.01    0.00    0.05    0.02    0.07    0.00    0.08    0.00    0.07    0.03    0.13    0.02    0.13    0.00    0.12    0.04    0.01    0.00    0.05    0.03    0.04    0.00    0.02    0.12    0.06    0.00    0.05    0.00    0.00    0.02    0.07    0.08    0.47    0.00    0.05    0.02    0.05    0.05    0.12    0.05    0.04    0.02    0.00    0.00    0.07    0.04    0.00    0.01    0.02    0.00    0.01    0.00    0.00    0.06    0.03  
SSTR5ENSG00000162009  0.01    0.00    0.02    0.00    0.00    0.00    0.02    0.01    0.02    0.15    0.00    0.00    0.04    0.02    0.05    0.05    0.04    0.09    0.03    0.03    0.03    0.12    0.05    0.08    0.03    0.04    0.03    0.03    0.01    0.02    0.05    0.06    0.00    0.05    0.20    0.02    0.00    0.02    0.00    0.00    0.08    0.02    0.11    0.19    0.10    0.05    0.03    0.04    0.19    0.21    0.08    0.05    0.00    0.01    0.00    0.00    0.00    0.04    0.01    0.00    0.02    0.02    0.00    0.00    0.05    0.02  
SLC39A14ENSG00000104635  0.00    0.02    0.00    0.00    0.00    0.01    0.00    0.23    0.00    0.14    0.00    0.00    0.00    0.03    0.00    0.07    0.00    0.09    0.00    0.06    0.01    0.07    0.04    0.04    0.00    0.12    0.01    0.17    0.00    0.06    0.05    0.13    0.00    0.05    0.03    0.00    0.01    0.02    0.00    0.00    0.01    0.17    0.00    0.43    0.00    0.05    0.01    0.11    0.07    0.24    0.05    0.06    0.03    0.00    0.00    0.00    0.00    0.11    0.00    0.01    0.01    0.02    0.00    0.01    0.01    0.04  
TNIKENSG00000154310  0.05    0.01    0.03    0.00    0.00    0.00    0.09    0.01    0.18    0.01    0.00    0.00    0.00    0.03    0.23    0.01    1.77    0.00    0.61    0.00    0.88    0.01    0.29    0.01    0.03    0.01    0.04    0.01    0.05    0.00    0.16    0.01    0.12    0.03    0.12    0.00    0.00    0.08    0.00    0.00    0.25    0.01    1.37    0.02    0.76    0.00    0.37    0.00    1.05    0.06    0.06    0.08    0.20    0.00    0.00    0.00    0.06    0.00    0.05    0.01    0.06    0.02    0.00    0.00    0.03    0.03  
CAMKK2ENSG00000110931  0.01    0.01    0.02    0.00    0.06    0.02    0.03    0.04    0.10    0.04    0.00    0.00    0.01    0.02    0.03    0.05    0.03    0.06    0.02    0.03    0.08    0.05    0.07    0.04    0.01    0.01    0.04    0.01    0.00    0.06    0.03    0.07    0.00    0.17    0.06    0.01    0.00    0.04    0.00    0.00    0.05    0.08    0.14    0.22    0.01    0.02    0.03    0.07    0.09    0.22    0.19    0.06    0.01    0.00    0.00    0.00    0.10    0.03    0.03    0.01    0.01    0.01    0.07    0.00    0.04    0.06  
NR6A1ENSG00000148200  0.00    0.00    0.01    0.00    0.00    0.00    0.03    0.01    0.02    0.03    0.00    0.01    0.00    0.02    0.04    0.02    0.05    0.03    0.07    0.01    0.11    0.02    0.08    0.01    0.02    0.01    0.05    0.02    0.00    0.01    0.03    0.03    0.06    0.04    0.10    0.04    0.00    0.00    0.00    0.00    0.07    0.03    0.11    0.15    0.02    0.01    0.02    0.04    0.10    0.16    0.13    0.04    0.02    0.02    0.01    0.00    0.05    0.00    0.02    0.00    0.04    0.03    0.00    0.03    0.03    0.04  

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