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 
cell adhesion molecule L1 likeENSG00000134121CHL1chr3:196596-409417:+  0    0.28    0    1  
CD177 moleculeENSG00000204936CD177chr19:43353659-43363172:+  0    0.28    0    1  
gamma-aminobutyric acid type A receptor subunit deltaENSG00000187730GABRDchr1:2019324-2030751:+  0    0.28    0    1  
ATPase secretory pathway Ca2+ transporting 2ENSG00000064270ATP2C2chr16:84368527-84464187:+  0    0.28    0    1  
tight junction protein 3ENSG00000105289TJP3chr19:3708109-3750813:+  0    0.28    0    1  
LY6/PLAUR domain containing 3ENSG00000124466LYPD3chr19:43460787-43465660:-  0    0.27    0    1  
solute carrier family 15 member 4ENSG00000139370SLC15A4chr12:128793191-128823983:-  0    0.27    0    2  
serine incorporator 1ENSG00000111897SERINC1chr6:122443354-122471822:-  0    0.27    0    2  
frizzled class receptor 3ENSG00000104290FZD3chr8:28494205-28574268:+  0    0.26    0    2  
FYN proto-oncogene, Src family tyrosine kinaseENSG00000010810FYNchr6:111660332-111873452:-  0    0.26    0    2  
teneurin transmembrane protein 3ENSG00000218336TENM3chr4:182143987-182803024:+  0    0.25    0    2  
golgi glycoprotein 1ENSG00000090863GLG1chr16:74447427-74607144:-  0    0.25    0    1  
protein O-mannosyltransferase 1ENSG00000130714POMT1chr9:131502902-131523806:+  0    0.25    0    1  
tumor suppressor candidate 3ENSG00000104723TUSC3chr8:15417215-15766649:+  0    0.25    0    2  
olfactomedin 1ENSG00000130558OLFM1chr9:135075243-135121179:+  0    0.25    0    1  
LysM domain containing 3ENSG00000176018LYSMD3chr5:90515611-90529584:-  0    0.25    0    2  
protein kinase C etaENSG00000027075PRKCHchr14:61187559-61550976:+  0    0.25    0    1  
presenilin 2ENSG00000143801PSEN2chr1:226870184-226896105:+  0    0.25    0    1  
solute carrier family 2 member 6ENSG00000160326SLC2A6chr9:133471095-133479137:-  0    0.25    0    1  
utrophinENSG00000152818UTRNchr6:144285701-144853034:+  0    0.24    0    2  

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