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 
PHRF1ENSG00000070047  0.01    0.00    0.00    0.00    0.01    0.03    0.01    0.02    0.01    0.14    0.00    0.00    0.02    0.05    0.03    0.08    0.02    0.16    0.03    0.07    0.03    0.15    0.04    0.07    0.01    0.03    0.01    0.03    0.03    0.06    0.07    0.04    0.03    0.01    0.04    0.10    0.02    0.06    0.00    0.00    0.03    0.13    0.06    0.50    0.01    0.07    0.05    0.09    0.18    0.18    0.03    0.23    0.02    0.07    0.00    0.00    0.05    0.00    0.01    0.11    0.01    0.07    0.00    0.00    0.02    0.03  
LRIG3ENSG00000139263  0.01    0.00    0.00    0.00    0.00    0.00    0.00    0.01    0.14    0.03    0.00    0.00    0.01    0.07    0.19    0.01    0.06    0.01    0.04    0.02    0.11    0.03    0.08    0.02    0.01    0.01    0.04    0.02    0.03    0.02    0.04    0.01    0.26    0.01    0.37    0.02    0.05    0.00    0.00    0.00    0.08    0.03    0.15    0.05    0.03    0.00    0.02    0.00    0.17    0.04    0.42    0.05    0.00    0.00    0.00    0.00    0.12    0.02    0.03    0.02    0.29    0.06    0.00    0.00    0.19    0.03  
EGFL6ENSG00000198759  0.00    0.00    0.01    0.00    0.00    0.00    0.03    0.00    0.05    0.04    0.00    0.00    0.00    0.00    0.03    0.05    0.08    0.05    0.02    0.02    0.07    0.03    0.06    0.03    0.02    0.01    0.13    0.02    0.02    0.01    0.02    0.02    0.00    0.01    0.02    0.01    0.01    0.00    0.01    0.00    0.05    0.03    0.15    0.18    0.06    0.00    0.04    0.02    0.10    0.10    0.09    0.06    0.06    0.01    0.00    0.00    0.00    0.04    0.02    0.01    0.02    0.00    0.00    0.00    0.05    0.02  
TGFB1ENSG00000105329  0.00    0.00    0.00    0.02    0.00    0.02    0.01    0.04    0.14    0.03    0.00    0.00    0.05    0.05    0.09    0.04    0.16    0.07    0.02    0.03    0.03    0.05    0.05    0.03    0.03    0.01    0.01    0.02    0.03    0.03    0.03    0.03    0.12    0.01    0.05    0.04    0.00    0.02    0.00    0.00    0.05    0.05    0.17    0.26    0.10    0.04    0.05    0.04    0.23    0.17    0.26    0.10    0.00    0.04    0.01    0.00    0.05    0.00    0.02    0.08    0.01    0.08    0.00    0.00    0.03    0.02  
MBTD1ENSG00000011258  0.01    0.00    0.05    0.00    0.00    0.00    0.03    0.02    0.14    0.01    0.01    0.00    0.11    0.00    0.10    0.01    0.12    0.01    0.02    0.01    0.17    0.00    0.11    0.01    0.03    0.01    0.07    0.03    0.06    0.04    0.07    0.01    0.02    0.01    0.05    0.03    0.01    0.01    0.00    0.00    0.47    0.03    0.17    0.03    0.08    0.00    0.09    0.02    0.19    0.02    0.13    0.01    0.02    0.00    0.00    0.00    0.00    0.00    0.03    0.01    0.03    0.00    0.03    0.03    0.17    0.01  
ADCK2ENSG00000133597  0.02    0.01    0.06    0.00    0.05    0.02    0.04    0.02    0.05    0.04    0.00    0.01    0.04    0.05    0.08    0.02    0.09    0.06    0.03    0.14    0.04    0.20    0.04    0.08    0.03    0.00    0.03    0.01    0.04    0.04    0.04    0.05    0.00    0.06    0.06    0.06    0.01    0.01    0.01    0.00    0.11    0.04    0.52    0.04    0.04    0.08    0.05    0.05    0.07    0.14    0.15    0.10    0.02    0.04    0.00    0.05    0.02    0.09    0.11    0.00    0.05    0.01    0.00    0.00    0.25    0.02  
INPP5KENSG00000132376  0.00    0.00    0.00    0.01    0.00    0.00    0.01    0.06    0.05    0.05    0.00    0.00    0.01    0.03    0.01    0.07    0.03    0.03    0.01    0.04    0.05    0.06    0.03    0.04    0.04    0.02    0.01    0.00    0.00    0.03    0.03    0.14    0.01    0.03    0.02    0.05    0.01    0.04    0.00    0.00    0.02    0.06    0.20    0.10    0.02    0.03    0.09    0.05    0.19    0.12    0.19    0.22    0.00    0.02    0.00    0.02    0.00    0.06    0.01    0.00    0.00    0.04    0.00    0.00    0.02    0.06  
SENP7ENSG00000138468  0.01    0.01    0.01    0.00    0.00    0.00    0.01    0.03    0.04    0.02    0.00    0.00    0.00    0.03    0.05    0.02    0.15    0.03    0.05    0.01    0.08    0.04    0.06    0.02    0.01    0.01    0.03    0.02    0.00    0.01    0.02    0.01    0.00    0.10    0.11    0.01    0.00    0.06    0.00    0.00    0.05    0.02    0.22    0.04    0.07    0.02    0.04    0.01    0.22    0.08    0.11    0.06    0.04    0.00    0.00    0.00    0.02    0.00    0.00    0.03    0.01    0.04    0.00    0.00    0.03    0.01  
SOAT1ENSG00000057252  0.02    0.00    0.01    0.01    0.00    0.00    0.01    0.03    0.22    0.01    0.02    0.00    0.07    0.03    0.11    0.00    0.18    0.01    0.03    0.00    0.17    0.03    0.10    0.01    0.03    0.00    0.13    0.00    0.04    0.00    0.16    0.01    0.20    0.01    0.00    0.04    0.02    0.00    0.00    0.00    0.16    0.01    0.35    0.04    0.08    0.01    0.08    0.00    0.25    0.00    0.27    0.03    0.07    0.00    0.00    0.00    0.32    0.00    0.01    0.00    0.01    0.01    0.02    0.00    0.10    0.02  
PORENSG00000127948  0.01    0.00    0.00    0.00    0.00    0.00    0.03    0.01    0.04    0.02    0.00    0.00    0.02    0.00    0.02    0.02    0.10    0.02    0.05    0.03    0.16    0.02    0.12    0.01    0.01    0.00    0.01    0.00    0.03    0.00    0.04    0.01    0.00    0.01    0.12    0.00    0.00    0.02    0.00    0.00    0.07    0.03    0.19    0.07    0.05    0.01    0.03    0.02    0.06    0.03    0.05    0.07    0.09    0.00    0.00    0.00    0.10    0.00    0.02    0.01    0.11    0.00    0.00    0.00    0.05    0.02  
EMC10ENSG00000161671  0.00    0.00    0.01    0.02    0.00    0.00    0.01    0.01    0.10    0.04    0.00    0.02    0.00    0.06    0.01    0.07    0.07    0.10    0.03    0.02    0.06    0.03    0.08    0.04    0.02    0.03    0.02    0.03    0.03    0.05    0.04    0.03    0.00    0.07    0.23    0.02    0.00    0.03    0.00    0.00    0.10    0.04    0.05    0.31    0.06    0.07    0.03    0.05    0.15    0.13    0.02    0.17    0.00    0.04    0.01    0.00    0.17    0.03    0.00    0.15    0.02    0.13    0.00    0.00    0.03    0.03  
CSNK1EENSG00000213923  0.00    0.00    0.00    0.01    0.00    0.00    0.01    0.00    0.09    0.05    0.00    0.05    0.00    0.03    0.07    0.03    0.10    0.02    0.03    0.01    0.03    0.02    0.03    0.02    0.01    0.02    0.03    0.02    0.02    0.02    0.08    0.00    0.00    0.01    0.02    0.01    0.00    0.04    0.00    0.00    0.04    0.03    0.12    0.11    0.03    0.02    0.09    0.02    0.23    0.10    0.06    0.03    0.01    0.03    0.00    0.00    0.00    0.00    0.01    0.01    0.02    0.03    0.02    0.00    0.22    0.01  
ZRANB2ENSG00000132485  0.00    0.02    0.01    0.02    0.00    0.00    0.01    0.07    0.06    0.06    0.00    0.00    0.00    0.09    0.05    0.07    0.04    0.06    0.01    0.05    0.02    0.06    0.02    0.04    0.00    0.10    0.01    0.06    0.00    0.01    0.02    0.04    0.00    0.12    0.04    0.03    0.00    0.18    0.00    0.00    0.04    0.07    0.13    0.16    0.03    0.04    0.02    0.03    0.00    0.06    0.19    0.04    0.01    0.06    0.02    0.01    0.00    0.03    0.00    0.01    0.02    0.03    0.03    0.05    0.02    0.06  
CHD8ENSG00000100888  0.00    0.01    0.00    0.03    0.00    0.00    0.00    0.03    0.09    0.06    0.00    0.00    0.00    0.05    0.14    0.02    0.14    0.08    0.09    0.07    0.09    0.07    0.09    0.05    0.03    0.02    0.01    0.07    0.01    0.05    0.08    0.00    0.00    0.02    0.29    0.03    0.01    0.02    0.00    0.00    0.09    0.03    0.39    0.10    0.08    0.01    0.07    0.04    0.16    0.10    0.17    0.08    0.02    0.01    0.00    0.01    0.00    0.00    0.03    0.03    0.01    0.10    0.00    0.00    0.03    0.02  
NLGN4XENSG00000146938  0.00    0.01    0.01    0.00    0.00    0.00    0.04    0.01    0.08    0.07    0.00    0.00    0.00    0.00    0.04    0.06    0.11    0.07    0.03    0.04    0.06    0.10    0.07    0.04    0.01    0.01    0.09    0.05    0.00    0.01    0.02    0.03    0.02    0.01    0.09    0.00    0.01    0.00    0.00    0.00    0.05    0.05    0.16    0.20    0.07    0.02    0.05    0.04    0.09    0.13    0.13    0.11    0.06    0.04    0.00    0.00    0.00    0.04    0.02    0.02    0.02    0.02    0.00    0.00    0.04    0.03  
PGGT1BENSG00000164219  0.21    0.01    0.03    0.01    0.02    0.01    0.01    0.12    0.04    0.07    0.00    0.01    0.00    0.08    0.02    0.07    0.00    0.07    0.01    0.05    0.02    0.07    0.02    0.13    0.01    0.12    0.01    0.08    0.00    0.03    0.07    0.04    0.05    0.02    0.15    0.02    0.00    0.03    0.00    0.00    0.02    0.06    0.10    0.36    0.00    0.05    0.01    0.03    0.04    0.08    0.13    0.04    0.01    0.00    0.00    0.09    0.04    0.02    0.00    0.02    0.01    0.01    0.00    0.03    0.04    0.07  
CDK13ENSG00000065883  0.01    0.00    0.01    0.01    0.00    0.00    0.01    0.01    0.07    0.02    0.00    0.00    0.00    0.00    0.03    0.01    0.04    0.03    0.04    0.01    0.10    0.04    0.02    0.00    0.03    0.00    0.00    0.00    0.00    0.00    0.01    0.01    0.00    0.01    0.13    0.00    0.00    0.00    0.01    0.00    0.06    0.02    0.10    0.08    0.01    0.00    0.05    0.01    0.09    0.03    0.07    0.03    0.04    0.00    0.00    0.02    0.00    0.02    0.01    0.00    0.03    0.00    0.00    0.00    0.04    0.03  
ING1ENSG00000153487  0.02    0.00    0.00    0.00    0.00    0.00    0.04    0.02    0.22    0.02    0.00    0.01    0.03    0.00    0.12    0.04    0.16    0.05    0.14    0.00    0.17    0.04    0.16    0.04    0.12    0.01    0.17    0.01    0.02    0.02    0.29    0.01    0.06    0.04    0.06    0.01    0.01    0.00    0.00    0.01    0.16    0.04    0.25    0.10    0.23    0.01    0.10    0.01    0.47    0.06    0.28    0.09    0.01    0.01    0.00    0.00    0.02    0.12    0.05    0.02    0.06    0.01    0.05    0.00    0.06    0.07  
ITGB2ENSG00000160255  0.00    0.00    0.01    0.00    0.00    0.00    0.01    0.04    0.05    0.04    0.00    0.02    0.00    0.01    0.03    0.02    0.03    0.05    0.02    0.06    0.04    0.08    0.03    0.07    0.02    0.03    0.02    0.08    0.01    0.01    0.03    0.03    0.05    0.07    0.01    0.05    0.01    0.00    0.00    0.00    0.10    0.02    0.20    0.18    0.05    0.03    0.06    0.02    0.06    0.14    0.07    0.11    0.04    0.00    0.10    0.00    0.00    0.00    0.01    0.00    0.02    0.02    0.05    0.00    0.02    0.03  
PHF21BENSG00000056487  0.00    0.00    0.01    0.00    0.00    0.05    0.01    0.05    0.02    0.09    0.00    0.04    0.00    0.04    0.04    0.08    0.05    0.05    0.01    0.03    0.02    0.02    0.04    0.05    0.00    0.03    0.01    0.11    0.01    0.08    0.04    0.05    0.00    0.05    0.00    0.03    0.00    0.06    0.00    0.00    0.05    0.05    0.01    0.46    0.04    0.05    0.02    0.10    0.06    0.32    0.05    0.11    0.00    0.03    0.00    0.00    0.00    0.09    0.00    0.05    0.00    0.08    0.00    0.00    0.18    0.04  

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