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).

 

List of the putative cancer-causing PDGs driven by SCNAs 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 
ENPP5ENSG00000112796                                                                                                                                                                                                                                                                        
LY86ENSG00000112799                                                                                                                                                                                                                                                                        
PRSS16ENSG00000112812                                                                                                                                                                                                                                                                        
BRD8ENSG00000112983  1                                                                                                                                                                                                                                                                    1  
HBEGFENSG00000113070                                                                                                                                                                                                                                                                      1  
SLC4A9ENSG00000113073                                                                                                                                                                                                                                                                        
LOXENSG00000113083  1                                                                                            1                                                                                                                                                                          
GZMKENSG00000113088                                                                                                                                                                                                                                                                        
SPARCENSG00000113140                                                                                                                                                                                                                                                                        
HMGCRENSG00000113161                                                                                      1                                                                                        1                                                                                          
PDE8BENSG00000113231                                                                                      1                                                                                        1                                                                                          
CLK4ENSG00000113240  1                                    1                                                                                                                                                                                                                                  
GRM6ENSG00000113262                                                                                                                                                                                                                                                                        
IL12BENSG00000113302                                                                                                                                                                                                                                                                        
BTNL8ENSG00000113303                                                                                                                                                                                                                                                                        
GABRG2ENSG00000113327                                                                                                                                                                                                                                                                        
TARSENSG00000113407                                                          1                                                                                                                                                                                                              
IL4ENSG00000113520                                                                                                                                                                                                                                                                        
IL5ENSG00000113525                                                                                                                                                                                                                                                                        
FGF1ENSG00000113578                                                                                                                                                                                                                                                                      1  

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