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 
HDAC10  ENSG00000100429    0    0    0.01    0.12    0.06    0.06    0.03    0.07    0.01    0.01    0    0.04    0    0.09    0.03    0.03    0    0.1    0.02    0.04    0    0.03    0    0    0.01    0.01    0    0    0    0.05    0.07    0.07    0.02    0.12    0.06    0.09    0    0.06    0.02    0.64    0.01    0.1    0    0.06    0.01    0.03    0.01    0.09    0.06    0.15    0.12    0.05    0.03    0.07    0    0.04    0    0.01    0    0.03    0.03    0.15    0.06    0.27    0    0  
HDAC6  ENSG00000094631    0.16    0    0.04    0.03    0.06    0.01    0.04    0.03    0    0.01    0    0    0.07    0    0.04    0.04    0.01    0    0.01    0.03    0    0    0.02    0    0.01    0    0    0    0    0    0    0    0.1    0.01    0.04    0.02    0    0    0.47    0.07    0.01    0    0.03    0    0.02    0    0.01    0    0.11    0    0.02    0    0.04    0    0.01    0    0    0    0    0    0.11    0.01    0.19    0.03    0.03    0  
HDAC7  ENSG00000061273    0.22    0.01    0.09    0.03    0.05    0.05    0.05    0    0    0.01    0.02    0    0.13    0.04    0.06    0.04    0.02    0.06    0.02    0.03    0    0    0    0    0.01    0    0    0.03    0.01    0.05    0.02    0.01    0.06    0.02    0.08    0.02    0    0.04    0.18    0.06    0    0.04    0.02    0.03    0    0.02    0.02    0.02    0.32    0.08    0.05    0.05    0.05    0.03    0.02    0.02    0    0    0    0    0.16    0.01    0.38    0.1    0    0  
HDAC4  ENSG00000068024    0.06    0.12    0    0.31    0.03    0.11    0.02    0.38    0.05    0.01    0.02    0.03    0.05    0    0.05    0.16    0    0.03    0.01    0.18    0    0.05    0.01    0.08    0.04    0.05    0    0    0    0.14    0.03    0.09    0.06    0.05    0.03    0.19    0    0.06    0.19    0.29    0.04    0.04    0    0.01    0.01    0.05    0.03    0.04    0.08    0.46    0.02    0.17    0.03    0.1    0.03    0.06    0    0.01    0    0.01    0.04    0.06    0.13    0.09    0.01    0.08  
HDAC5  ENSG00000108840    0.07    0.14    0.04    0.03    0.03    0.1    0.02    0.03    0.08    0.01    0.02    0.01    0    0    0.12    0.02    0    0.02    0.02    0.01    0    0    0    0    0    0    0    0    0    0.01    0.04    0.03    0.07    0.01    0.04    0.05    0.02    0    0.02    0.13    0.05    0.01    0    0.1    0.01    0.17    0.03    0.03    0.06    0.06    0.01    0.06    0.08    0.03    0.01    0.01    0    0    0.01    0    0.05    0.07    0.09    0.19    0    0.05  
HDAC9  ENSG00000048052    0.11    0    0.25    0.01    0.09    0.04    0.03    0.01    0    0.01    0.05    0    0.06    0.06    0.17    0.04    0.05    0    0.07    0.01    0    0    0.01    0    0.01    0.01    0    0.02    0    0.01    0.05    0.01    0.11    0.01    0.12    0.01    0.08    0    0.17    0.27    0.01    0    0    0.03    0.03    0.03    0.03    0    0.16    0.03    0.13    0.02    0.08    0.03    0.08    0    0    0    0    0    0.08    0.04    0.04    0.08    0    0  
SIRT6  ENSG00000077463    0.04    0.01    0.02    0.13    0.05    0.11    0.04    0.19    0    0.03    0    0.04    0    0.03    0.06    0.11    0.05    0.01    0.03    0.11    0    0.04    0    0.01    0    0.02    0.04    0    0.01    0.02    0.05    0.13    0.01    0.08    0.02    0.12    0.01    0.1    0.03    0.82    0    0.06    0.01    0    0.01    0.03    0.01    0.1    0.14    0.07    0.04    0.06    0.01    0.09    0    0    0    0.01    0.02    0    0.01    0.27    0    0.74    0    0.05  
SIRT3  ENSG00000142082    0.04    0.07    0.01    0.13    0.03    0.14    0.01    0.07    0.03    0.01    0.01    0.03    0.05    0    0.02    0.15    0.03    0.07    0.03    0.08    0.01    0.03    0.01    0    0    0    0    0    0.01    0.11    0.07    0.03    0.03    0.08    0.02    0.16    0.02    0.05    0.06    0.5    0.03    0.06    0.02    0.07    0    0.02    0.01    0.03    0.03    0.26    0.02    0.03    0.04    0.07    0.02    0.07    0    0    0    0    0.06    0.1    0.11    0.18    0    0  
SIRT1  ENSG00000096717    0    0.01    0.01    0.04    0.07    0.04    0    0.01    0.25    0.04    0.03    0.03    0    0    0.05    0.05    0    0.02    0.03    0.02    0.03    0    0    0    0    0.01    0    0    0    0    0.02    0.03    0.04    0.03    0.06    0.03    0.03    0    0.11    0.11    0.01    0    0    0    0.02    0.03    0.07    0.03    0.02    0.12    0    0.01    0.08    0.02    0    0    0    0.01    0    0    0.04    0.03    0.09    0.05    0    0  
SIRT2  ENSG00000068903    0.05    0.03    0.32    0.02    0.14    0.03    0.29    0.03    0.12    0.01    0.05    0.01    0.03    0    0.1    0.03    0.05    0.04    0.07    0.01    0    0.02    0    0    0.01    0.01    0.01    0    0.04    0.04    0.05    0.02    0.2    0.03    0.53    0.03    0.08    0.02    0.76    0.12    0.27    0    0    0.02    0.02    0.03    0.03    0.01    0.24    0.1    0.04    0.01    0.09    0.02    0    0.03    0    0    0    0    0.18    0.03    1.1    0.09    0    0  
SIRT7  ENSG00000187531    0.27    0    0.22    0    0.33    0.05    0.1    0.09    0.15    0.01    0.05    0    0    0    0.12    0.1    0.04    0.02    0.07    0.06    0.02    0    0.02    0    0.05    0    0    0    0.07    0.01    0.31    0.01    0.17    0.02    0.19    0.07    0.12    0.02    0.41    0.06    0.02    0.09    0.03    0.01    0.03    0.02    0.04    0.02    0.18    0.11    0.24    0.03    0.11    0.04    0.06    0.01    0    0    0    0    0.18    0.01    0.74    0.08    0.14    0  
SIRT4  ENSG00000089163    0.13    0.01    0.09    0.04    0.04    0.08    0.01    0.02    0    0.17    0    0.01    0.1    0    0.11    0.05    0.01    0    0.03    0.02    0.06    0.02    0.01    0.01    0.02    0    0    0    0.03    0.01    0.03    0.07    0.03    0.05    0.03    0.05    0.01    0.02    0.14    0.2    0    0.06    0    0.03    0.04    0.04    0.04    0.01    0.13    0.04    0.02    0.06    0.07    0.02    0.01    0    0    0    0    0    0.05    0.04    0.09    0.08    0.07    0  
SIRT5  ENSG00000124523    0.01    0.01    0.41    0.04    0.19    0.03    0.09    0.05    0.06    0.03    0.02    0.03    0.05    0.04    0.13    0.17    0.01    0.02    0.05    0.05    0    0    0    0    0    0.01    0    0    0.01    0.03    0.15    0.01    0.08    0.01    0.09    0.07    0.02    0.02    0.51    0.05    0    0.07    0    0.01    0.01    0.01    0.01    0.03    0.06    0.13    0.22    0    0.03    0.09    0.04    0.03    0    0    0    0.01    0.07    0.02    0.28    0.02    0.25    0  

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