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 
zinc and ring finger 3ENSG00000183579ZNRF3chr22:28883592-29057487:+  0    0.67    0    1  
plexin B1ENSG00000164050PLXNB1chr3:48403854-48430051:-  0    0.67    0    4  
microtubule associated protein 4ENSG00000047849MAP4chr3:47850690-48089272:-  0    0.66    0    4  
agrinENSG00000188157AGRNchr1:1020123-1056118:+  0    0.66    0    3  
solute carrier family 23 member 3ENSG00000213901SLC23A3chr2:219161465-219170095:-  0    0.66    0    3  
PX domain containing serine/threonine kinase likeENSG00000168297PXKchr3:58332880-58426126:+  0    0.66    0    4  
cell adhesion molecule 1ENSG00000182985CADM1chr11:115169218-115504957:-  0    0.66    0    3  
layilinENSG00000204381LAYNchr11:111540280-111561745:+  0    0.65    0    3  
fibronectin type III domain containing 10ENSG00000228594C1orf233chr1:1598012-1600096:-  0    0.65    0    4  
dopamine receptor D4ENSG00000069696DRD4chr11:637293-640706:+  0    0.65    0    2  
junctional adhesion molecule 3ENSG00000166086JAM3chr11:134068925-134152001:+  0    0.65    0    3  
oligodendrocyte myelin glycoproteinENSG00000126861OMGchr17:31272013-31297539:-  0    0.64    0    2  
ATPase Na+/K+ transporting subunit alpha 1ENSG00000163399ATP1A1chr1:116372668-116410261:+  0    0.64    0    4  
myelin protein zero like 3ENSG00000160588MPZL3chr11:118226690-118252350:-  0    0.64    0    3  
delta like canonical Notch ligand 1ENSG00000198719DLL1chr6:170282206-170306565:-  0    0.63    0    2  
zinc finger FYVE-type containing 27ENSG00000155256ZFYVE27chr10:97737121-97760907:+  0    0.62    0    3  
synaptosome associated protein 23ENSG00000092531SNAP23chr15:42491233-42545356:+  0    0.62    0    3  
major facilitator superfamily domain containing 14AENSG00000156875HIAT1chr1:100038097-100083377:+  0    0.62    0    3  
transmembrane 9 superfamily member 3ENSG00000077147TM9SF3chr10:96518109-96587452:-  0    0.62    0    3  
calcium homeostasis modulator family member 2ENSG00000138172CALHM2chr10:103446786-103452402:-  0    0.61    0    3  

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