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).

 

List 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 
ADAM metallopeptidase domain 28ENSG00000042980ADAM28chr8:24294040-24359018:+              1                                                                                                                                                                                                                                                          
cholinergic receptor nicotinic epsilon subunitENSG00000108556CHRNEchr17:4897774-4903074:-                                                                                                                              1                                                                                                                                          
endomucinENSG00000164035EMCNchr4:100395341-100880126:-                                                                                                                              1                                                                                                                                          
leucine rich repeat containing 8 VRAC subunit DENSG00000171492LRRC8Dchr1:89821014-89936611:+                                                                                                                                                                                                              1                                                          
solute carrier family 7 member 2ENSG00000003989SLC7A2chr8:17497088-17570573:+                                                                                                                              1                                                                                                                                          
gamma-aminobutyric acid type A receptor subunit beta3ENSG00000166206GABRB3chr15:26543546-26939539:-                                                                                                                                      1                                                                                                                                  
solute carrier family 18 member A1ENSG00000036565SLC18A1chr8:20144855-20183206:-                                              1                                                                                                                                                                                                                          
melanoma cell adhesion moleculeENSG00000076706MCAMchr11:119308529-119321521:-              1                                                                                                                                                                                                                                                          
melanotransferrinENSG00000163975MFI2chr3:196988621-197029816:-                                                                                                                                                                                                      1                                                                  
non-compact myelin associated proteinENSG00000184454NCMAPchr1:24556111-24609328:+                                                                                                                                              1                                                                                                                          
macrophage scavenger receptor 1ENSG00000038945MSR1chr8:16107878-16567490:-                                                                                                                              1                                                                                                                                          
solute carrier family 39 member 8ENSG00000138821SLC39A8chr4:102251041-102431258:-                                                                                                                              1                                                                                                                                          
transmembrane protein 63CENSG00000165548TMEM63Cchr14:77116568-77259495:+                                                                                                                      1                                                                                                                                                  
zinc finger DHHC-type palmitoyltransferase 22ENSG00000177108ZDHHC22chr14:77131270-77142734:-                                                                                                                      1                                                                                                                                                  
APC membrane recruitment protein 1ENSG00000184675AMER1chrX:64185117-64205744:-                                                              1                                                                                                                                                                                                          
TNF receptor superfamily member 9ENSG00000049249TNFRSF9chr1:7915894-7943165:-                                                                                                                                              1                                                                                                                          
cerebral endothelial cell adhesion moleculeENSG00000167123CERCAMchr9:128411751-128437351:+                                                                                                                                                                                                                                                              1          
leucine rich repeat containing 8 VRAC subunit AENSG00000136802LRRC8Achr9:128882112-128918039:+                                                                                                                                                                                                                                                              1          
mitoguardin 2ENSG00000148343FAM73Bchr9:129036621-129072082:+                                                                                                                                                                                                                                                              1          
MAPK associated protein 1ENSG00000119487MAPKAP1chr9:125437393-125707234:-                                                                                                                                                                                                                                                              1          

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