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 
transmembrane p24 trafficking protein 10ENSG00000170348TMED10chr14:75131470-75176631:-  0    0.5    0    3  
transient receptor potential cation channel subfamily M member 4ENSG00000130529TRPM4chr19:49157741-49211836:+  0    0.49    0    2  
Fc fragment of IgG receptor and transporterENSG00000104870FCGRTchr19:49506816-49526333:+  0    0.49    0    2  
receptor activity modifying protein 1ENSG00000132329RAMP1chr2:237858893-237912114:+  0    0.49    0    2  
prostaglandin F2 receptor inhibitorENSG00000134247PTGFRNchr1:116910057-116990358:+  0    0.49    0    3  
phosphatidylinositol 4-kinase type 2 alphaENSG00000155252PI4K2Achr10:97640686-97676434:+  0    0.49    0    2  
SPG11 vesicle trafficking associated, spatacsinENSG00000104133SPG11chr15:44562696-44663678:-  0    0.49    0    2  
pleckstrin and Sec7 domain containingENSG00000059915PSDchr10:102402617-102421539:-  0    0.49    0    2  
vasodilator stimulated phosphoproteinENSG00000125753VASPchr19:45506579-45526983:+  0    0.49    0    2  
heat shock protein family A (Hsp70) member 8ENSG00000109971HSPA8chr11:123057489-123063230:-  0    0.48    0    2  
membrane associated guanylate kinase, WW and PDZ domain containing 3ENSG00000081026MAGI3chr1:113390749-113685923:+  0    0.48    0    3  
zinc finger DHHC-type palmitoyltransferase 20ENSG00000180776ZDHHC20chr13:21372573-21459370:-  0    0.48    0    3  
sortilin related receptor 1ENSG00000137642SORL1chr11:121452203-121633693:+  0    0.48    0    2  
membrane palmitoylated protein 5ENSG00000072415MPP5chr14:67241109-67335819:+  0    0.48    0    3  
basigin (Ok blood group)ENSG00000172270BSGchr19:571277-583493:+  0    0.47    0    3  
interferon induced transmembrane protein 2ENSG00000185201IFITM2chr11:307631-315272:+  0    0.47    0    3  
G protein subunit alpha i3ENSG00000065135GNAI3chr1:109548611-109618321:+  0    0.47    0    2  
glycoprotein integral membrane 1ENSG00000055211GINM1chr6:149566294-149591748:+  0    0.47    0    3  
leucine rich repeats and immunoglobulin like domains 2ENSG00000198799LRIG2chr1:113073209-113132260:+  0    0.47    0    3  
colony stimulating factor 1ENSG00000184371CSF1chr1:109910242-109930992:+  0    0.47    0    2  

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