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 
secretory carrier membrane protein 4ENSG00000227500SCAMP4chr19:1905214-1926013:+  0    0.94    0    2  
sorting nexin 9ENSG00000130340SNX9chr6:157700387-157945077:+  0    0.94    0    4  
transmembrane protein 181ENSG00000146433TMEM181chr6:158536436-158635428:+  0    0.94    0    4  
integral membrane protein 2BENSG00000136156ITM2Bchr13:48233158-48270357:+  0    0.93    0    4  
CD58 moleculeENSG00000116815CD58chr1:116514535-116571039:-  0    0.93    0    5  
EPS8 like 2ENSG00000177106EPS8L2chr11:694438-727727:+  0    0.92    0    4  
InaF motif containing 2ENSG00000259330INAFM2chr15:40325216-40326715:+  0    0.92    0    4  
endothelin converting enzyme like 1ENSG00000171551ECEL1chr2:232479827-232487828:-  0    0.91    0    3  
transmembrane protein 171ENSG00000157111TMEM171chr5:73120292-73131817:+  0    0.87    0    2  
beta-secretase 1ENSG00000186318BACE1chr11:117285207-117316259:-  0    0.86    0    4  
HYLS1 centriolar and ciliogenesis associatedENSG00000198331HYLS1chr11:125883614-125900648:+  0    0.86    0    4  
F2R like trypsin receptor 1ENSG00000164251F2RL1chr5:76818933-76835315:+  0    0.85    0    2  
TNF receptor superfamily member 14ENSG00000157873TNFRSF14chr1:2555639-2565382:+  0    0.84    0    4  
sterol-C5-desaturaseENSG00000109929SC5Dchr11:121292453-121308694:+  0    0.83    0    4  
secretory carrier membrane protein 1ENSG00000085365SCAMP1chr5:78360583-78479071:+  0    0.83    0    2  
osteoclastogenesis associated transmembrane protein 1ENSG00000081087OSTM1chr6:108041409-108165854:-  0    0.81    0    5  
anoctamin 9ENSG00000185101ANO9chr11:417933-442011:-  0    0.8    0    3  
plakophilin 3ENSG00000184363PKP3chr11:392614-404908:+  0    0.8    0    3  
transmembrane protein 25ENSG00000149582TMEM25chr11:118531041-118547280:+  0    0.8    0    4  
ATPase cation transporting 13A2ENSG00000159363ATP13A2chr1:16985958-17011928:-  0    0.79    0    4  

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