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 
uronyl 2-sulfotransferaseENSG00000111962USTchr6:148747328-149076990:+  0.56    0.13    1    1  
extended synaptotagmin 2ENSG00000117868ESYT2chr7:158730995-158830253:-  0.56    0.82    1    4  
3'(2'), 5'-bisphosphate nucleotidase 2ENSG00000104331IMPAD1chr8:56957933-56993844:-  0.56    0    3    0  
oxidized low density lipoprotein receptor 1ENSG00000173391OLR1chr12:10158301-10172138:-  0.56    0    1    0  
C-type lectin domain family 1 member AENSG00000150048CLEC1Achr12:10069554-10111627:-  0.56    0    1    0  
serine/threonine/tyrosine kinase 1ENSG00000060140STYK1chr12:10618939-10674318:-  0.56    0    1    0  
taste 2 receptor member 14ENSG00000212127TAS2R14chr12:10937406-11171573:-  0.55    0.16    1    1  
taste 2 receptor member 19ENSG00000212124TAS2R19chr12:11021619-11022620:-  0.55    0    1    0  
taste 2 receptor member 31ENSG00000256436TAS2R31chr12:11030387-11031407:-  0.55    0    1    0  
vesicle associated membrane protein 7ENSG00000124333VAMP7chrX:155881293-155943769:+  0.55    0    3    0  
LDL receptor related protein 12ENSG00000147650LRP12chr8:104489231-104589024:-  0.55    0    2    0  
zinc finger DHHC-type palmitoyltransferase 4ENSG00000136247ZDHHC4chr7:6577434-6589374:+  0.55    0.39    4    1  
tyrosine kinase non receptor 2ENSG00000061938TNK2chr3:195863364-195911945:-  0.55    0.14    2    1  
transferrin receptorENSG00000072274TFRCchr3:196027183-196082189:-  0.55    0.14    2    1  
ryanodine receptor 1ENSG00000196218RYR1chr19:38433699-38587564:+  0.54    0    1    0  
discs large MAGUK scaffold protein 5ENSG00000151208DLG5chr10:77790791-77926526:-  0.54    0    2    0  
carbonic anhydrase 14ENSG00000118298CA14chr1:150257159-150265078:+  0.54    0    3    0  
RAB8A, member RAS oncogene familyENSG00000167461RAB8Achr19:16111629-16134234:+  0.54    0    2    0  
solute carrier family 15 member 1ENSG00000088386SLC15A1chr13:98683801-98752654:-  0.53    0    3    0  
BLK proto-oncogene, Src family tyrosine kinaseENSG00000136573BLKchr8:11494001-11564604:+  0.53    0    1    0  

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