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).
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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 3 | ENSG00000183579 | ZNRF3 | chr22:28883592-29057487:+ | 0 | 0.67 | 0 | 1 |
plexin B1 | ENSG00000164050 | PLXNB1 | chr3:48403854-48430051:- | 0 | 0.67 | 0 | 4 |
microtubule associated protein 4 | ENSG00000047849 | MAP4 | chr3:47850690-48089272:- | 0 | 0.66 | 0 | 4 |
agrin | ENSG00000188157 | AGRN | chr1:1020123-1056118:+ | 0 | 0.66 | 0 | 3 |
solute carrier family 23 member 3 | ENSG00000213901 | SLC23A3 | chr2:219161465-219170095:- | 0 | 0.66 | 0 | 3 |
PX domain containing serine/threonine kinase like | ENSG00000168297 | PXK | chr3:58332880-58426126:+ | 0 | 0.66 | 0 | 4 |
cell adhesion molecule 1 | ENSG00000182985 | CADM1 | chr11:115169218-115504957:- | 0 | 0.66 | 0 | 3 |
layilin | ENSG00000204381 | LAYN | chr11:111540280-111561745:+ | 0 | 0.65 | 0 | 3 |
fibronectin type III domain containing 10 | ENSG00000228594 | C1orf233 | chr1:1598012-1600096:- | 0 | 0.65 | 0 | 4 |
dopamine receptor D4 | ENSG00000069696 | DRD4 | chr11:637293-640706:+ | 0 | 0.65 | 0 | 2 |
junctional adhesion molecule 3 | ENSG00000166086 | JAM3 | chr11:134068925-134152001:+ | 0 | 0.65 | 0 | 3 |
oligodendrocyte myelin glycoprotein | ENSG00000126861 | OMG | chr17:31272013-31297539:- | 0 | 0.64 | 0 | 2 |
ATPase Na+/K+ transporting subunit alpha 1 | ENSG00000163399 | ATP1A1 | chr1:116372668-116410261:+ | 0 | 0.64 | 0 | 4 |
myelin protein zero like 3 | ENSG00000160588 | MPZL3 | chr11:118226690-118252350:- | 0 | 0.64 | 0 | 3 |
delta like canonical Notch ligand 1 | ENSG00000198719 | DLL1 | chr6:170282206-170306565:- | 0 | 0.63 | 0 | 2 |
zinc finger FYVE-type containing 27 | ENSG00000155256 | ZFYVE27 | chr10:97737121-97760907:+ | 0 | 0.62 | 0 | 3 |
synaptosome associated protein 23 | ENSG00000092531 | SNAP23 | chr15:42491233-42545356:+ | 0 | 0.62 | 0 | 3 |
major facilitator superfamily domain containing 14A | ENSG00000156875 | HIAT1 | chr1:100038097-100083377:+ | 0 | 0.62 | 0 | 3 |
transmembrane 9 superfamily member 3 | ENSG00000077147 | TM9SF3 | chr10:96518109-96587452:- | 0 | 0.62 | 0 | 3 |
calcium homeostasis modulator family member 2 | ENSG00000138172 | CALHM2 | chr10:103446786-103452402:- | 0 | 0.61 | 0 | 3 |
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