Copy Number

 

The putative cancer-associated GESPs 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 putative cancer-causing GESPs driven by SCNAs in each cancer type


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ACCBLCABRCACESCCHOLCOADDLBCESCAGBMHNSCKICHKIRCKIRPLAMLLGGLIHCLUADLUSCMESOOVPAADPCPGPRADREADSARCSKCMSTADTGCTTHCATHYMUCECUCSUVM
 HGNC Name  Ensembl Gene ID  HGNC Symbol  Genomic Location  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 
UL16 binding protein 2ENSG00000131015ULBP2chr6:149942000-149949235:+                                                                                                                                                                                                              0.13                                                          
LDL receptor related protein 11ENSG00000120256LRP11chr6:149818798-149864026:-                                                                                                                                                                                                              0.13                                                          
UL16 binding protein 3ENSG00000131019ULBP3chr6:150063150-150069095:-                                                                                                                                                                                                              0.13                                                          
adhesion G protein-coupled receptor A1ENSG00000197177ADGRA1chr10:133070929-133131675:+                                                                                                                      0.13                                                                                                                                                  
protein tyrosine phosphatase receptor type KENSG00000152894PTPRKchr6:127968779-128520674:-                                                                                                                                                                                                              0.13                                                          
vanin 2ENSG00000112303VNN2chr6:132743870-132763459:-                                                                                                                                                                                                              0.13                                                          
protein tyrosine phosphatase receptor type EENSG00000132334PTPREchr10:127907061-128085855:+                                                                                                                      0.13                                                                                                                                                  
sortilin 1ENSG00000134243SORT1chr1:109309568-109397951:-                                                                                                                                      0.13                                                                                                                                  
cadherin EGF LAG seven-pass G-type receptor 2ENSG00000143126CELSR2chr1:109250019-109275750:+                                                                                                                                      0.13                                                                                                                                  
adhesion molecule with Ig like domain 1ENSG00000181754AMIGO1chr1:109504175-109509738:-                                                                                                                                      0.13                                                                                                                                  
eukaryotic translation elongation factor 1 alpha 1ENSG00000156508EEF1A1chr6:73515750-73523797:-                                                                                                                                                                                                      0.13                                                                  
vanin 1ENSG00000112299VNN1chr6:132681590-132714049:-                                                                                                                                                                                                              0.13                                                          
leucine rich repeat transmembrane neuronal 2ENSG00000146006LRRTM2chr5:138868923-138875368:-                                                                                                                                                                                                              0.13                                                          
G protein-coupled receptor kinase 5ENSG00000198873GRK5chr10:119207589-119459742:+                                                                                                                      0.13                                                                                                                                                  
polypeptide N-acetylgalactosaminyltransferase 10ENSG00000164574GALNT10chr5:154190730-154420984:+                                                                                                                                                                                                              0.13                                                          
G protein-coupled receptor 26ENSG00000154478GPR26chr10:123666355-123694607:+                                                                                                                      0.13                                                                                                                                                  
ubiquitin conjugating enzyme E2 D3ENSG00000109332UBE2D3chr4:102794383-102868896:-                                                                                                                              0.13                                                                                                                                          
repulsive guidance molecule BMP co-receptor bENSG00000174136RGMBchr5:98768650-98798643:+                                                                                                                                                                                                                      0.13                                                  
complement C1q binding proteinENSG00000108561C1QBPchr17:5432777-5448830:-                                                                                                                              0.13                                                                                                                                          
CD226 moleculeENSG00000150637CD226chr18:69831158-69961803:-                                              0.13                                                                                                                                                                                                                          

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