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 
discoidin, CUB and LCCL domain containing 1ENSG00000164465DCBLD1chr6:117453817-117569858:+  0    0.24    0    2  
netrin G2ENSG00000196358NTNG2chr9:132161676-132244534:+  0    0.24    0    1  
synaptotagmin like 1ENSG00000142765SYTL1chr1:27342020-27353937:+  0    0.24    0    1  
transmembrane protein 30BENSG00000182107TMEM30Bchr14:61277370-61281840:-  0    0.24    0    1  
interleukin 6 signal transducerENSG00000134352IL6STchr5:55935095-55994993:-  0    0.24    0    1  
potassium sodium-activated channel subfamily T member 1ENSG00000107147KCNT1chr9:135702185-135795508:+  0    0.24    0    1  
chromosome 1 open reading frame 162ENSG00000143110C1orf162chr1:111473792-111478512:+  0    0.24    0    2  
contactin associated protein family member 3ENSG00000106714CNTNAP3chr9:39072767-39288315:-  0    0.24    0    2  
neural cell adhesion molecule 1ENSG00000149294NCAM1chr11:112961247-113278436:+  0    0.24    0    1  
solute carrier family 38 member 6ENSG00000139974SLC38A6chr14:60981114-61083733:+  0    0.24    0    1  
peptidylglycine alpha-amidating monooxygenaseENSG00000145730PAMchr5:102753981-103031105:+  0    0.24    0    2  
CD53 moleculeENSG00000143119CD53chr1:110873154-110899928:+  0    0.24    0    2  
potassium voltage-gated channel subfamily C member 4ENSG00000116396KCNC4chr1:110211343-110283100:+  0    0.23    0    2  
neuronal calcium sensor 1ENSG00000107130NCS1chr9:130172578-130237304:+  0    0.23    0    1  
family with sequence similarity 174 member AENSG00000174132FAM174Achr5:100535305-100586741:+  0    0.23    0    2  
G protein-coupled receptor 135ENSG00000181619GPR135chr14:59429022-59465342:-  0    0.23    0    1  
pecanex 4ENSG00000126773PCNXL4chr14:60091911-60169133:+  0    0.23    0    1  
interleukin 10 receptor subunit alphaENSG00000110324IL10RAchr11:117986348-118001483:+  0    0.23    0    1  
junction adhesion molecule likeENSG00000160593AMICA1chr11:118193740-118225094:-  0    0.23    0    1  
transforming growth factor beta receptor 3ENSG00000069702TGFBR3chr1:91680343-91906335:-  0    0.23    0    2  

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