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).

 

Pan-cancer level overall G-score of GESPs that recurrently gained or lost copy number in at least one cancer types


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Overall_Gscore No. of Cancer Types
 HGNC Name  Ensembl Gene ID  HGNC Symbol  Genomic Location  Amplification  Deletion  Amplification  Deletion 
ADAM metallopeptidase domain 28ENSG00000042980ADAM28chr8:24294040-24359018:+  0    0.12    0    1  
cholinergic receptor nicotinic epsilon subunitENSG00000108556CHRNEchr17:4897774-4903074:-  0    0.12    0    1  
endomucinENSG00000164035EMCNchr4:100395341-100880126:-  0    0.12    0    1  
leucine rich repeat containing 8 VRAC subunit DENSG00000171492LRRC8Dchr1:89821014-89936611:+  0    0.12    0    1  
solute carrier family 7 member 2ENSG00000003989SLC7A2chr8:17497088-17570573:+  0    0.12    0    1  
gamma-aminobutyric acid type A receptor subunit beta3ENSG00000166206GABRB3chr15:26543546-26939539:-  0    0.12    0    1  
solute carrier family 18 member A1ENSG00000036565SLC18A1chr8:20144855-20183206:-  0    0.12    0    1  
melanoma cell adhesion moleculeENSG00000076706MCAMchr11:119308529-119321521:-  0    0.12    0    1  
melanotransferrinENSG00000163975MFI2chr3:196988621-197029816:-  0    0.12    0    1  
non-compact myelin associated proteinENSG00000184454NCMAPchr1:24556111-24609328:+  0    0.12    0    1  
macrophage scavenger receptor 1ENSG00000038945MSR1chr8:16107878-16567490:-  0    0.12    0    1  
solute carrier family 39 member 8ENSG00000138821SLC39A8chr4:102251041-102431258:-  0    0.12    0    1  
transmembrane protein 63CENSG00000165548TMEM63Cchr14:77116568-77259495:+  0    0.11    0    1  
zinc finger DHHC-type palmitoyltransferase 22ENSG00000177108ZDHHC22chr14:77131270-77142734:-  0    0.11    0    1  
APC membrane recruitment protein 1ENSG00000184675AMER1chrX:64185117-64205744:-  0    0.11    0    1  
TNF receptor superfamily member 9ENSG00000049249TNFRSF9chr1:7915894-7943165:-  0    0.11    0    1  
cerebral endothelial cell adhesion moleculeENSG00000167123CERCAMchr9:128411751-128437351:+  0    0.11    0    1  
leucine rich repeat containing 8 VRAC subunit AENSG00000136802LRRC8Achr9:128882112-128918039:+  0    0.11    0    1  
mitoguardin 2ENSG00000148343FAM73Bchr9:129036621-129072082:+  0    0.11    0    1  
MAPK associated protein 1ENSG00000119487MAPKAP1chr9:125437393-125707234:-  0    0.11    0    1  

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