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
 HGNC Symbol  Ensembl 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 
TNFRSF11AENSG00000141655  0.00    0.01    0.00    0.00    0.00    0.00    0.00    0.10    0.01    0.08    0.00    0.00    0.00    0.02    0.02    0.10    0.05    0.06    0.02    0.14    0.06    0.22    0.02    0.16    0.00    0.12    0.00    0.10    0.01    0.08    0.02    0.06    0.00    0.10    0.00    0.03    0.01    0.00    0.00    0.00    0.08    0.05    0.08    0.33    0.01    0.03    0.01    0.07    0.01    0.11    0.11    0.07    0.00    0.07    0.00    0.00    0.11    0.00    0.01    0.02    0.00    0.04    0.00    0.01    0.03    0.01  
HSPG2ENSG00000142798  0.00    0.05    0.00    0.08    0.00    0.00    0.02    0.03    0.08    0.09    0.00    0.01    0.04    0.23    0.05    0.06    0.05    0.11    0.03    0.08    0.03    0.10    0.08    0.12    0.00    0.16    0.00    0.21    0.01    0.08    0.01    0.22    0.00    1.06    0.09    0.04    0.01    0.10    0.00    0.00    0.02    0.19    0.14    0.44    0.05    0.09    0.07    0.13    0.24    0.21    0.17    0.10    0.05    0.06    0.02    0.00    0.00    0.11    0.00    0.02    0.04    0.11    0.00    0.12    0.05    0.08  
COL11A1ENSG00000060718  0.00    0.01    0.00    0.01    0.00    0.00    0.01    0.06    0.02    0.07    0.00    0.00    0.00    0.33    0.02    0.12    0.02    0.10    0.01    0.09    0.03    0.09    0.02    0.07    0.00    0.08    0.01    0.06    0.00    0.02    0.01    0.03    0.00    0.11    0.04    0.04    0.00    0.25    0.00    0.00    0.03    0.11    0.13    0.17    0.02    0.07    0.03    0.03    0.01    0.06    0.05    0.09    0.03    0.05    0.00    0.01    0.00    0.07    0.01    0.01    0.01    0.04    0.00    0.03    0.06    0.11  
CHST11ENSG00000171310  0.01    0.01    0.02    0.00    0.06    0.02    0.04    0.02    0.07    0.03    0.00    0.00    0.04    0.02    0.02    0.05    0.02    0.04    0.02    0.03    0.04    0.05    0.04    0.03    0.01    0.01    0.01    0.04    0.00    0.06    0.04    0.04    0.00    0.22    0.01    0.02    0.00    0.03    0.00    0.00    0.04    0.08    0.07    0.22    0.01    0.01    0.02    0.04    0.02    0.11    0.20    0.04    0.00    0.01    0.00    0.00    0.10    0.03    0.01    0.02    0.01    0.01    0.00    0.00    0.02    0.08  
NSD1ENSG00000165671  0.34    0.01    0.07    0.02    0.00    0.00    0.04    0.00    0.02    0.11    0.00    0.01    0.03    0.05    0.10    0.04    0.05    0.06    0.02    0.09    0.13    0.02    0.04    0.04    0.03    0.02    0.04    0.03    0.03    0.02    0.16    0.02    0.05    0.01    0.51    0.02    0.01    0.03    0.01    0.00    0.11    0.03    0.27    0.12    0.03    0.05    0.09    0.02    0.32    0.01    0.15    0.08    0.00    0.01    0.00    0.03    0.02    0.00    0.01    0.06    0.03    0.04    0.04    0.00    0.09    0.09  
IL6STENSG00000134352  0.01    0.00    0.00    0.01    0.05    0.00    0.01    0.24    0.07    0.13    0.00    0.00    0.01    0.01    0.07    0.06    0.03    0.10    0.03    0.09    0.02    0.14    0.02    0.11    0.02    0.06    0.01    0.06    0.00    0.05    0.03    0.01    0.00    0.10    0.07    0.01    0.00    0.03    0.00    0.00    0.03    0.11    0.04    0.52    0.03    0.07    0.02    0.12    0.01    0.33    0.08    0.05    0.00    0.02    0.00    0.03    0.00    0.00    0.00    0.01    0.00    0.01    0.00    0.00    0.03    0.03  
DNMT1ENSG00000130816  0.00    0.00    0.00    0.01    0.00    0.00    0.01    0.02    0.10    0.04    0.00    0.01    0.09    0.01    0.03    0.04    0.08    0.06    0.05    0.05    0.08    0.06    0.05    0.04    0.02    0.01    0.01    0.04    0.01    0.03    0.04    0.11    0.00    0.01    0.13    0.03    0.01    0.00    0.00    0.01    0.10    0.04    0.60    0.20    0.11    0.06    0.20    0.08    0.64    0.21    0.31    0.03    0.02    0.00    0.03    0.00    0.00    0.03    0.01    0.00    0.05    0.00    0.04    0.02    0.03    0.01  
ACACBENSG00000076555  0.01    0.01    0.02    0.00    0.06    0.02    0.04    0.03    0.09    0.03    0.00    0.00    0.02    0.00    0.02    0.05    0.02    0.04    0.02    0.03    0.09    0.05    0.05    0.02    0.00    0.01    0.01    0.02    0.00    0.06    0.03    0.04    0.00    0.22    0.11    0.01    0.00    0.03    0.00    0.00    0.03    0.07    0.09    0.20    0.01    0.02    0.01    0.05    0.08    0.07    0.13    0.06    0.00    0.01    0.00    0.00    0.10    0.00    0.00    0.04    0.01    0.02    0.00    0.00    0.02    0.07  
LMTK3ENSG00000142235  0.00    0.00    0.00    0.02    0.00    0.00    0.01    0.04    0.07    0.04    0.00    0.02    0.00    0.08    0.01    0.08    0.04    0.10    0.02    0.02    0.05    0.05    0.06    0.03    0.01    0.02    0.01    0.03    0.04    0.05    0.04    0.04    0.00    0.07    0.18    0.02    0.00    0.03    0.00    0.00    0.06    0.05    0.07    0.33    0.06    0.07    0.04    0.06    0.14    0.22    0.03    0.18    0.00    0.04    0.01    0.00    0.07    0.03    0.00    0.13    0.01    0.13    0.00    0.00    0.03    0.02  
CDH3ENSG00000062038  0.00    0.00    0.01    0.00    0.00    0.06    0.01    0.11    0.17    0.02    0.00    0.00    0.00    0.07    0.05    0.03    0.05    0.02    0.03    0.02    0.16    0.05    0.04    0.06    0.00    0.01    0.03    0.01    0.01    0.00    0.01    0.04    0.09    0.01    0.21    0.06    0.01    0.01    0.00    0.01    0.03    0.05    0.03    0.35    0.03    0.04    0.02    0.09    0.07    0.14    0.02    0.05    0.14    0.02    0.02    0.04    0.00    0.03    0.00    0.00    0.00    0.03    0.00    0.03    0.05    0.01  
PSMA3ENSG00000100567  0.00    0.02    0.00    0.00    0.00    0.00    0.00    0.02    0.02    0.04    0.00    0.01    0.00    0.05    0.08    0.02    0.03    0.04    0.05    0.01    0.06    0.01    0.04    0.04    0.00    0.02    0.02    0.02    0.03    0.00    0.03    0.06    0.05    0.10    0.04    0.03    0.01    0.01    0.00    0.00    0.05    0.05    0.03    0.22    0.01    0.02    0.01    0.02    0.00    0.06    0.03    0.09    0.00    0.01    0.00    0.00    0.04    0.03    0.00    0.06    0.01    0.05    0.03    0.00    0.01    0.04  
LPAR1ENSG00000198121  0.00    0.00    0.01    0.00    0.00    0.00    0.03    0.01    0.07    0.04    0.00    0.00    0.02    0.02    0.05    0.02    0.05    0.02    0.05    0.01    0.09    0.03    0.05    0.02    0.00    0.01    0.05    0.02    0.00    0.01    0.02    0.05    0.06    0.11    0.08    0.04    0.00    0.00    0.00    0.00    0.03    0.05    0.09    0.12    0.02    0.01    0.01    0.04    0.00    0.15    0.08    0.01    0.04    0.02    0.00    0.00    0.04    0.02    0.00    0.01    0.02    0.01    0.00    0.00    0.04    0.01  
PPIL4ENSG00000131013  0.00    0.06    0.00    0.01    0.00    0.05    0.00    0.03    0.04    0.08    0.00    0.03    0.00    0.17    0.01    0.06    0.05    0.05    0.03    0.04    0.08    0.04    0.09    0.05    0.02    0.01    0.04    0.04    0.00    0.03    0.01    0.12    0.00    0.16    0.15    0.03    0.00    0.02    0.00    0.00    0.10    0.07    0.02    0.41    0.02    0.07    0.03    0.04    0.08    0.03    0.35    0.02    0.01    0.04    0.00    0.00    0.00    0.09    0.00    0.05    0.01    0.09    0.00    0.09    0.01    0.13  
SLC1A5ENSG00000105281  0.00    0.00    0.00    0.02    0.00    0.00    0.00    0.04    0.08    0.04    0.00    0.02    0.00    0.08    0.02    0.08    0.05    0.11    0.02    0.02    0.06    0.04    0.08    0.03    0.01    0.03    0.01    0.02    0.03    0.04    0.02    0.04    0.00    0.10    0.13    0.04    0.00    0.02    0.00    0.00    0.05    0.07    0.05    0.33    0.06    0.07    0.02    0.06    0.11    0.19    0.03    0.18    0.00    0.04    0.01    0.00    0.26    0.09    0.00    0.13    0.01    0.13    0.00    0.00    0.02    0.03  
MTAPENSG00000099810  0.00    0.09    0.01    0.15    0.00    0.06    0.00    0.06    0.03    1.01    0.00    0.12    0.00    1.35    0.03    0.55    0.03    0.78    0.05    0.81    0.03    1.30    0.02    0.35    0.02    0.05    0.01    0.03    0.03    0.65    0.01    0.25    0.00    0.45    0.00    0.30    0.00    0.01    0.00    0.01    0.05    0.16    0.08    0.21    0.06    0.05    0.05    0.02    0.04    0.05    0.05    0.53    0.02    0.02    0.00    0.01    0.00    0.75    0.00    0.42    0.01    1.83    0.00    0.00    0.01    1.06  
ITGB1ENSG00000150093  0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.02    0.04    0.05    0.00    0.01    0.03    0.02    0.07    0.01    0.05    0.01    0.05    0.02    0.14    0.01    0.13    0.01    0.01    0.00    0.00    0.00    0.00    0.00    0.03    0.00    0.03    0.01    0.01    0.04    0.00    0.00    0.00    0.00    0.04    0.02    0.24    0.04    0.01    0.01    0.03    0.01    0.22    0.00    0.03    0.02    0.00    0.00    0.00    0.00    0.00    0.00    0.01    0.00    0.00    0.01    0.00    0.00    0.01    0.02  
PPP1CAENSG00000172531  0.01    0.00    0.00    0.00    0.09    0.00    0.10    0.00    0.22    0.01    0.00    0.00    0.08    0.00    0.15    0.01    0.18    0.01    0.44    0.01    0.40    0.02    0.16    0.02    0.01    0.01    0.05    0.02    0.02    0.01    0.15    0.01    0.20    0.02    0.08    0.01    0.03    0.00    0.00    0.00    0.50    0.03    0.28    0.03    0.21    0.00    0.18    0.02    0.29    0.02    0.13    0.03    0.00    0.04    0.00    0.00    0.00    0.06    0.01    0.01    0.01    0.03    0.00    0.00    0.20    0.02  
CACNA2D3ENSG00000157445  0.00    0.15    0.00    0.02    0.00    0.02    0.00    0.03    0.05    0.15    0.00    0.03    0.00    0.52    0.01    0.05    0.01    0.13    0.00    0.09    0.00    0.26    0.02    0.09    0.00    0.05    0.02    0.06    0.00    0.05    0.01    0.06    0.00    0.20    0.06    0.01    0.01    0.02    0.00    0.00    0.01    0.17    0.08    0.20    0.01    0.12    0.01    0.08    0.00    0.38    0.05    0.15    0.06    0.01    0.00    0.01    0.00    0.08    0.01    0.04    0.00    0.05    0.00    0.06    0.05    0.04  
ATP5A1ENSG00000152234  0.00    0.00    0.00    0.00    0.00    0.00    0.01    0.03    0.07    0.05    0.00    0.00    0.02    0.03    0.03    0.08    0.10    0.02    0.08    0.05    0.17    0.12    0.02    0.11    0.01    0.07    0.01    0.02    0.01    0.07    0.01    0.04    0.00    0.05    0.00    0.02    0.00    0.00    0.00    0.00    0.04    0.03    0.18    0.17    0.01    0.02    0.05    0.03    0.24    0.00    0.12    0.04    0.01    0.03    0.00    0.00    0.00    0.00    0.00    0.02    0.00    0.03    0.00    0.01    0.03    0.01  
FN1ENSG00000115414  0.02    0.06    0.04    0.03    0.00    0.03    0.02    0.03    0.02    0.26    0.00    0.00    0.00    0.12    0.03    0.03    0.03    0.19    0.01    0.18    0.03    0.11    0.05    0.04    0.02    0.02    0.02    0.02    0.06    0.03    0.03    0.04    0.00    0.01    0.03    0.00    0.00    0.01    0.00    0.01    0.05    0.05    0.17    0.16    0.03    0.33    0.03    0.04    0.08    0.05    0.06    0.18    0.08    0.01    0.00    0.00    0.00    0.04    0.00    0.02    0.00    0.00    0.02    0.02    0.02    0.04  

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