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 
sushi domain containing 6ENSG00000100647SUSD6chr14:69611596-69715142:+  0    0.61    0    4  
ras homolog family member CENSG00000155366RHOCchr1:112701106-112707434:-  0    0.61    0    3  
inositol 1,4,5-trisphosphate receptor interacting proteinENSG00000148841ITPRIPchr10:104309698-104338404:-  0    0.61    0    3  
tight junction protein 1ENSG00000104067TJP1chr15:29699367-29968865:-  0    0.61    0    5  
tectonic family member 3ENSG00000119977TCTN3chr10:95663396-95694143:-  0    0.6    0    3  
GRAM domain containing 1BENSG00000023171GRAMD1Bchr11:123454398-123627774:+  0    0.59    0    3  
CD151 molecule (Raph blood group)ENSG00000177697CD151chr11:832843-839831:+  0    0.57    0    4  
patatin like phospholipase domain containing 2ENSG00000177666PNPLA2chr11:818902-825573:+  0    0.57    0    4  
hyaluronidase 2ENSG00000068001HYAL2chr3:50317790-50322906:-  0    0.56    0    3  
presenilin 1ENSG00000080815PSEN1chr14:73136418-73223691:+  0    0.55    0    3  
EPH receptor A2ENSG00000142627EPHA2chr1:16124337-16156087:-  0    0.53    0    3  
semaphorin 3BENSG00000012171SEMA3Bchr3:50267558-50277546:+  0    0.53    0    3  
myelin protein zero like 2ENSG00000149573MPZL2chr11:118253403-118264536:-  0    0.53    0    2  
neural proliferation, differentiation and control 1ENSG00000107281NPDC1chr9:137039470-137046203:-  0    0.52    0    3  
piezo type mechanosensitive ion channel component 1ENSG00000103335PIEZO1chr16:88715343-88785211:-  0    0.52    0    4  
ATP binding cassette subfamily B member 6 (Langereis blood group)ENSG00000115657ABCB6chr2:219209768-219218990:-  0    0.52    0    2  
solute carrier family 19 member 3ENSG00000135917SLC19A3chr2:227685210-227718012:-  0    0.52    0    2  
protein tyrosine kinase 2 betaENSG00000120899PTK2Bchr8:27311482-27459391:+  0    0.51    0    4  
fukutin related proteinENSG00000181027FKRPchr19:46746046-46776988:+  0    0.51    0    2  
interleukin 17 receptor BENSG00000056736IL17RBchr3:53846580-53865800:+  0    0.5    0    3  

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