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 
RAS guanyl releasing protein 1ENSG00000172575RASGRP1chr15:38488103-38565575:-  0    0.78    0    4  
solute carrier family 26 member 6ENSG00000225697SLC26A6chr3:48625723-48635493:-  0    0.78    0    5  
CD164 moleculeENSG00000135535CD164chr6:109366514-109382559:-  0    0.78    0    5  
insulin like growth factor 2 receptorENSG00000197081IGF2Rchr6:159969099-160113507:+  0    0.77    0    3  
pannexin 2ENSG00000073150PANX2chr22:50170731-50180294:+  0    0.77    0    2  
ezrinENSG00000092820EZRchr6:158765741-158819412:-  0    0.77    0    3  
atypical chemokine receptor 3ENSG00000144476ACKR3chr2:236567787-236582358:+  0    0.77    0    3  
TNF receptor superfamily member 10dENSG00000173530TNFRSF10Dchr8:23135588-23164030:-  0    0.76    0    5  
protein tyrosine phosphatase receptor type DENSG00000153707PTPRDchr9:8314246-10612723:-  0    0.76    0    4  
signal peptide peptidase like 2BENSG00000005206SPPL2Bchr19:2328615-2354806:+  0    0.75    0    1  
shadow of prion proteinENSG00000203772SPRNchr10:133420666-133424572:-  0    0.75    0    5  
occludinENSG00000197822OCLNchr5:69492292-69558104:+  0    0.74    0    1  
cadherin EGF LAG seven-pass G-type receptor 3ENSG00000008300CELSR3chr3:48636469-48662915:-  0    0.73    0    4  
TNF receptor superfamily member 25ENSG00000215788TNFRSF25chr1:6461151-6466195:-  0    0.73    0    4  
G protein subunit alpha i2ENSG00000114353GNAI2chr3:50226292-50259355:+  0    0.71    0    4  
dystroglycan 1ENSG00000173402DAG1chr3:49468703-49535618:+  0    0.71    0    4  
RALBP1 associated Eps domain containing 1ENSG00000135597REPS1chr6:138903493-138988261:-  0    0.7    0    5  
cyclin and CBS domain divalent metal cation transport mediator 2ENSG00000148842CNNM2chr10:102918293-103090221:+  0    0.7    0    4  
coagulation factor II thrombin receptorENSG00000181104F2Rchr5:76716043-76735781:+  0    0.7    0    1  
serine incorporator 5ENSG00000164300SERINC5chr5:80111651-80256079:-  0    0.67    0    1  

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