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 
interleukin 17 receptor AENSG00000177663IL17RAchr22:17084954-17115694:+  0    0.13    0    1  
solute carrier family 12 member 2ENSG00000064651SLC12A2chr5:128083766-128189688:+  0    0.13    0    1  
microfibril associated protein 3ENSG00000037749MFAP3chr5:154038906-154220478:+  0    0.13    0    1  
SLP adaptor and CSK interacting membrane proteinENSG00000161929SCIMPchr17:5208961-5234860:-  0    0.13    0    1  
reticulon 4 receptor like 1ENSG00000185924RTN4RL1chr17:1934677-2025345:-  0    0.13    0    1  
CXADR Ig-like cell adhesion moleculeENSG00000154639CXADRchr21:17512382-17593579:+  0    0.13    0    1  
solute carrier family 9 member B2ENSG00000164038SLC9B2chr4:103019868-103085829:-  0    0.13    0    1  
roundabout guidance receptor 1ENSG00000169855ROBO1chr3:78597240-79767815:-  0    0.13    0    1  
C-X-C motif chemokine ligand 16ENSG00000161921CXCL16chr17:4733526-4739922:-  0    0.12    0    1  
protocadherin 9ENSG00000184226PCDH9chr13:66302834-67230445:-  0    0.12    0    1  
leucyl and cystinyl aminopeptidaseENSG00000113441LNPEPchr5:96935394-97037515:+  0    0.12    0    1  
prolactin releasing hormone receptorENSG00000119973PRLHRchr10:118589989-118595699:-  0    0.12    0    1  
cystinosin, lysosomal cystine transporterENSG00000040531CTNSchr17:3636468-3661542:+  0    0.12    0    1  
integrin subunit alpha EENSG00000083457ITGAEchr17:3714628-3801243:-  0    0.12    0    1  
sphingolipid transporter 3 (putative)ENSG00000182557SPNS3chr17:4433688-4488208:+  0    0.12    0    1  
transient receptor potential cation channel subfamily V member 1ENSG00000196689TRPV1chr17:3565444-3597098:-  0    0.12    0    1  
adenosine A2b receptorENSG00000170425ADORA2Bchr17:15944917-15975746:+  0    0.12    0    1  
monooxygenase DBH like 1ENSG00000079931MOXD1chr6:132296055-132401545:-  0    0.12    0    1  
sphingomyelin synthase 2ENSG00000164023SGMS2chr4:107824563-107915047:+  0    0.12    0    1  
teneurin transmembrane protein 2ENSG00000145934TENM2chr5:167284799-168264157:+  0    0.12    0    1  

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