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 
programmed cell death 1ENSG00000188389PDCD1chr2:241849881-241858908:-  0    0.32    0    1  
fms related receptor tyrosine kinase 3 ligandENSG00000090554FLT3LGchr19:49474207-49486231:+  0    0.31    0    1  
ankyrin repeat and sterile alpha motif domain containing 1BENSG00000185046ANKS1Bchr12:98726457-99984654:-  0    0.31    0    1  
gap junction protein alpha 3ENSG00000121743GJA3chr13:20138255-20161049:-  0    0.31    0    2  
Fas cell surface death receptorENSG00000026103FASchr10:88990531-89015785:+  0    0.31    0    1  
tetraspanin 2ENSG00000134198TSPAN2chr1:115048011-115089500:-  0    0.31    0    2  
CD81 moleculeENSG00000110651CD81chr11:2376177-2397419:+  0    0.31    0    2  
sortilin related VPS10 domain containing receptor 1ENSG00000108018SORCS1chr10:106573663-107164534:-  0    0.3    0    1  
podoplaninENSG00000162493PDPNchr1:13583465-13617957:+  0    0.3    0    2  
sorbin and SH3 domain containing 1ENSG00000095637SORBS1chr10:95311771-95561414:-  0    0.3    0    1  
interferon induced transmembrane protein 1ENSG00000185885IFITM1chr11:313506-315272:+  0    0.3    0    2  
protein tyrosine phosphatase non-receptor type 22ENSG00000134242PTPN22chr1:113813811-113871759:-  0    0.3    0    2  
beta-2-microglobulinENSG00000166710B2Mchr15:44711477-44718877:+  0    0.29    0    2  
LY6/PLAUR domain containing 5ENSG00000159871LYPD5chr19:43795929-43827206:-  0    0.29    0    1  
CEA cell adhesion molecule 19ENSG00000186567CEACAM19chr19:44662278-44684359:+  0    0.29    0    1  
solute carrier family 16 member 1ENSG00000155380SLC16A1chr1:112911847-112957013:-  0    0.29    0    2  
basal cell adhesion molecule (Lutheran blood group)ENSG00000187244BCAMchr19:44809059-44821420:+  0    0.29    0    1  
plasminogen activator, urokinase receptorENSG00000011422PLAURchr19:43646095-43670547:-  0    0.28    0    1  
protein kinase C and casein kinase substrate in neurons 2ENSG00000100266PACSIN2chr22:42835412-43015145:-  0    0.28    0    1  
FER tyrosine kinaseENSG00000151422FERchr5:108747822-109196841:+  0    0.28    0    2  

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