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 
UL16 binding protein 2ENSG00000131015ULBP2chr6:149942000-149949235:+  0    0.13    0    1  
LDL receptor related protein 11ENSG00000120256LRP11chr6:149818798-149864026:-  0    0.13    0    1  
UL16 binding protein 3ENSG00000131019ULBP3chr6:150063150-150069095:-  0    0.13    0    1  
adhesion G protein-coupled receptor A1ENSG00000197177ADGRA1chr10:133070929-133131675:+  0    0.13    0    1  
protein tyrosine phosphatase receptor type KENSG00000152894PTPRKchr6:127968779-128520674:-  0    0.13    0    1  
vanin 2ENSG00000112303VNN2chr6:132743870-132763459:-  0    0.13    0    1  
protein tyrosine phosphatase receptor type EENSG00000132334PTPREchr10:127907061-128085855:+  0    0.13    0    1  
sortilin 1ENSG00000134243SORT1chr1:109309568-109397951:-  0    0.13    0    1  
cadherin EGF LAG seven-pass G-type receptor 2ENSG00000143126CELSR2chr1:109250019-109275750:+  0    0.13    0    1  
adhesion molecule with Ig like domain 1ENSG00000181754AMIGO1chr1:109504175-109509738:-  0    0.13    0    1  
eukaryotic translation elongation factor 1 alpha 1ENSG00000156508EEF1A1chr6:73515750-73523797:-  0    0.13    0    1  
vanin 1ENSG00000112299VNN1chr6:132681590-132714049:-  0    0.13    0    1  
leucine rich repeat transmembrane neuronal 2ENSG00000146006LRRTM2chr5:138868923-138875368:-  0    0.13    0    1  
G protein-coupled receptor kinase 5ENSG00000198873GRK5chr10:119207589-119459742:+  0    0.13    0    1  
polypeptide N-acetylgalactosaminyltransferase 10ENSG00000164574GALNT10chr5:154190730-154420984:+  0    0.13    0    1  
G protein-coupled receptor 26ENSG00000154478GPR26chr10:123666355-123694607:+  0    0.13    0    1  
ubiquitin conjugating enzyme E2 D3ENSG00000109332UBE2D3chr4:102794383-102868896:-  0    0.13    0    1  
repulsive guidance molecule BMP co-receptor bENSG00000174136RGMBchr5:98768650-98798643:+  0    0.13    0    1  
complement C1q binding proteinENSG00000108561C1QBPchr17:5432777-5448830:-  0    0.13    0    1  
CD226 moleculeENSG00000150637CD226chr18:69831158-69961803:-  0    0.13    0    1  

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