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 
CECR2  ENSG00000099954    0.06    0.07    0.15    0.06    0.06    0.06    0.05    0.01    0.08    0.1    0.01    0.02    0    0    0.06    0.13    0.01    0.03    0.06    0.04    0    0    0    0    0    0.01    0.01    0    0.01    0.01    0.02    0.04    0.06    0.04    0.14    0.08    0.07    0.05    0.15    0.1    0    0.02    0    0.01    0.01    0.04    0.06    0.03    0.11    0.06    0.1    0.03    0.05    0.04    0.1    0.04    0.02    0    0.03    0    0.06    0.05    0.34    0.09    0    0  
KIAA2026  ENSG00000183354    0.12    0.08    0.17    0.12    0.1    0.06    0.21    0.04    0.03    0.01    0.01    0.03    0.04    0.02    0.17    0.15    0.01    0.2    0.25    0.06    0    0    0    0    0    0.02    0    0    0    0.09    0.06    0.03    0.05    0.12    0.16    0.1    0.04    0.05    0.17    0.2    0    0.08    0.01    0.02    0    0.05    0.04    0.05    0.24    0.12    0.05    0.11    0.14    0.11    0.01    0.09    0    0    0.01    0.01    0.08    0.03    0.02    0.12    0    0  
BRD1  ENSG00000100425    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  
BRPF3  ENSG00000096070    0.21    0    0.07    0.04    0.07    0.03    0.08    0    0.05    0.03    0.02    0.01    0.08    0    0.15    0.04    0.02    0    0.02    0.03    0    0    0    0    0.01    0.01    0    0    0.01    0    0.05    0.04    0.08    0.01    0.03    0.05    0.02    0.01    0.26    0.05    0.01    0.01    0    0    0.01    0.01    0.06    0.01    0.07    0.07    0.09    0.01    0.07    0.03    0.05    0.01    0    0    0    0    0.06    0.01    0.22    0.07    0.1    0  
BRPF1  ENSG00000156983    0.08    0.01    0.42    0.02    0.12    0.02    0.02    0.01    0    0.18    0    0.04    0    0.05    0.09    0.05    0.03    0.02    0.03    0.02    0.07    0    0    0.18    0    0.01    0    0    0.04    0.01    0.07    0.01    0.05    0.05    0.03    0.03    0.05    0.06    0.18    0.21    0.01    0.02    0    0.04    0.01    0.06    0.01    0.06    0.24    0.03    0.02    0.06    0.07    0.06    0.05    0.05    0    0    0    0.03    0.05    0.03    0.18    0.14    0    0  
BRD7  ENSG00000166164    0.06    0.04    0.04    0.03    0.05    0.06    0.02    0.06    0    0.13    0.04    0.01    0    0.04    0.08    0.01    0    0.04    0.03    0.04    0    0    0    0.01    0    0    0.02    0    0    0    0    0.02    0.06    0.04    0.06    0.02    0    0.06    0.07    0.14    0.01    0    0    0.03    0.01    0.08    0.01    0    0.02    0.13    0.01    0.06    0.02    0.04    0.08    0.01    0    0    0    0    0.02    0.05    0.05    0.14    0    0.03  
BRD9  ENSG00000028310    0.81    0.03    0.27    0.01    0.13    0.02    0.22    0.02    0    0.05    0.04    0.02    0.17    0    0.37    0.03    0.05    0.03    0.16    0.01    0.03    0.03    0.01    0    0.03    0.01    0    0    0.01    0.06    0.25    0.01    0.42    0.01    0.39    0.01    0.06    0    0.48    0.04    0.03    0.01    0.01    0    0.03    0.01    0.06    0.02    0.32    0.13    0.31    0.07    0.18    0.01    0.03    0.03    0    0    0    0.01    0.16    0.01    0.26    0.03    0.03    0.02  
BAZ2A  ENSG00000076108    0.32    0.02    0.04    0.03    0.04    0.04    0.03    0    0    0.01    0.02    0    0.12    0    0.08    0.04    0.1    0.05    0.01    0.02    0    0    0    0    0    0    0    0    0.02    0.03    0.05    0.01    0.11    0.01    0.03    0.01    0.02    0.02    0.21    0.04    0.03    0.01    0.07    0    0.01    0.01    0.02    0.01    0.13    0.07    0.1    0.03    0.07    0.02    0.02    0    0    0    0    0    0.06    0    0.28    0.06    0    0  
BAZ2B  ENSG00000123636    0.02    0.02    0.11    0.06    0.04    0.04    0.05    0.02    0    0.05    0.01    0.02    0    0.15    0.1    0.04    0    0.01    0.04    0.03    0    0    0.02    0    0.01    0    0    0    0    0    0.05    0.06    0.04    0.01    0.1    0.03    0    0    0.34    0.05    0.05    0.01    0    0    0.02    0.1    0.01    0.01    0.05    0.1    0.03    0.01    0.03    0.05    0.03    0.01    0    0    0    0.01    0.07    0.01    0.06    0.04    0    0  
ATAD2  ENSG00000156802    0.18    0    0.28    0.03    0.53    0.02    0.17    0.01    0.25    0.01    0.19    0    0.13    0    0.62    0.01    0.04    0.01    0.27    0    0.09    0    0.02    0    0.01    0    0.02    0    0.21    0    0.4    0.01    0.28    0.01    0.33    0.01    0.05    0.01    1.46    0.03    0.14    0    0.01    0.01    0.08    0.01    0.25    0    0.19    0.05    0.19    0.01    0.29    0.01    0.03    0.02    0    0    0.02    0    0.2    0.01    0.34    0    0.55    0  
ATAD2B  ENSG00000119778    0.01    0.06    0.09    0.01    0.05    0.04    0.08    0    0    0.05    0.01    0    0.02    0.03    0.06    0.06    0.02    0.03    0.03    0.02    0    0    0    0    0.02    0.01    0    0    0.01    0.01    0.08    0.02    0.06    0.01    0.08    0.03    0.03    0.08    0.18    0.13    0.01    0.04    0.01    0    0.02    0.01    0.01    0.02    0.06    0.1    0.03    0.04    0.03    0.03    0.17    0.01    0    0    0    0    0.12    0.03    0.26    0.03    0.05    0  
BRD8  ENSG00000112983    0.24    0.02    0.03    0.03    0.03    0.02    0.03    0.01    0.09    0.01    0.01    0.02    0.04    0    0.03    0.03    0.01    0.02    0.01    0.03    0    0    0.28    0    0.03    0.02    0    0.1    0.01    0.04    0.09    0.02    0.01    0.04    0.02    0.03    0.03    0.03    0.13    0.12    0.01    0.01    0    0.06    0.03    0.03    0.02    0.02    0.08    0.04    0.03    0.12    0.01    0.05    0    0    0.01    0    0    0    0.03    0.01    0.15    0.01    0    0.03  
BRWD3  ENSG00000165288    0.07    0.01    0.02    0.03    0.03    0.02    0.01    0.02    0    0.01    0.02    0.01    0.01    0.06    0.07    0.06    0.01    0.01    0.03    0.01    0    0.01    0    0    0    0    0    0    0.02    0    0    0    0.04    0.02    0.07    0.03    0    0    0.1    0.04    0.01    0.01    0    0    0.01    0.01    0    0.01    0.15    0.11    0.03    0.01    0.03    0.01    0    0    0    0    0    0    0.03    0.02    0.03    0    0    0.02  
BRWD1  ENSG00000185658    0.01    0.04    0.05    0.04    0.11    0.02    0.09    0.02    0.07    0.03    0.01    0.02    0    0    0.02    0.09    0    0.02    0.02    0.05    0    0    0    0    0    0    0.15    0    0    0.01    0.02    0.01    0.05    0.02    0.03    0.06    0    0    0.14    0.12    0.01    0.01    0.01    0    0.02    0.29    0    0.08    0.07    0.07    0.01    0.02    0.03    0.07    0.04    0    0    0    0    0    0.04    0.01    0.04    0.03    0.03    0  
PHIP  ENSG00000146247    0.06    0.02    0.03    0.08    0.07    0.08    0.03    0.01    0    0.21    0    0.02    0    0.29    0.03    0.07    0    0.04    0.03    0.04    0    0    0    0.01    0    0    0    0    0    0    0.03    0.05    0.03    0.04    0.1    0.03    0.01    0.03    0.15    0.11    0    0.02    0.01    0    0    0.2    0.01    0.01    0.07    0.14    0.02    0.04    0.04    0.07    0.04    0    0    0    0    0    0.02    0.01    0.08    0.06    0.04    0.03  
HDAC1  ENSG00000116478    0    0.03    0.03    0.07    0.05    0.09    0.06    0.02    0    0.61    0.02    0.09    0    0.1    0.05    0.07    0.02    0.04    0.05    0.05    0    0    0    0.04    0    0.06    0.02    0    0    0.01    0.01    0.17    0.05    0.04    0.04    0.06    0.11    0.07    0.31    0.23    0.01    0.03    0.02    0.07    0.03    0.02    0.01    0.11    0.14    0.05    0.05    0.05    0.05    0.07    0.03    0.03    0    0    0    0.01    0.07    0.07    0.06    0.05    0    0.07  
HDAC2  ENSG00000196591    0.02    0.04    0.01    0.12    0.09    0.09    0.01    0.02    0    0.12    0.01    0.03    0.01    0.18    0.06    0.07    0    0.08    0.02    0.03    0    0    0    0.04    0    0    0    0    0    0.04    0.01    0.07    0.01    0.05    0.03    0.05    0    0.16    0.06    0.28    0    0.04    0    0.01    0.01    0.28    0.01    0.06    0.15    0.05    0    0.14    0.03    0.06    0    0.04    0    0    0    0.01    0.04    0.02    0.05    0.03    0    0.03  
HDAC3  ENSG00000171720    0.22    0.02    0.02    0.03    0.03    0.02    0.03    0.01    0.09    0.01    0.01    0.01    0.04    0    0.02    0.03    0.01    0.02    0.01    0.03    0    0    0.3    0    0.03    0.01    0    0.1    0    0.05    0.07    0.03    0.02    0.04    0.01    0.03    0    0.04    0.14    0.11    0.02    0.03    0    0.05    0.03    0.02    0.02    0.01    0.07    0.04    0.01    0.15    0.02    0.04    0    0    0.01    0    0    0    0.02    0.02    0.11    0.01    0    0.03  
HDAC8  ENSG00000147099    0.01    0    0.04    0.02    0.02    0.02    0.03    0.02    0    0.01    0.01    0.01    0.01    0.05    0.12    0.02    0.01    0    0.03    0.01    0    0.01    0    0    0.01    0    0    0    0.03    0.01    0    0.01    0.04    0.02    0.05    0.04    0    0.02    0.18    0.02    0    0    0    0    0.02    0    0    0.02    0.16    0.07    0.02    0.01    0.04    0.02    0    0    0    0    0    0    0.04    0.01    0.08    0    0    0  
HDAC11  ENSG00000163517    0.08    0.01    0.46    0.01    0.12    0.03    0.04    0.01    0    0.18    0.01    0.03    0    0.05    0.05    0.02    0.01    0.02    0.03    0.02    0.07    0    0    0.18    0    0.01    0    0    0.03    0.01    0.06    0.01    0.03    0.05    0.02    0.03    0.03    0.07    0.15    0.22    0.01    0.02    0    0.04    0.01    0.02    0.03    0.06    0.25    0.01    0.02    0.05    0.05    0.05    0.04    0.05    0    0    0    0.03    0.14    0.04    0.35    0.14    0    0  

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