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 |
| solute carrier family 7 member 6 | ENSG00000103064 | SLC7A6 | chr16:68264516-68301823:+ | 0.16 | 0.32 | 1 | 1 |
| potassium voltage-gated channel modifier subfamily S member 3 | ENSG00000170745 | KCNS3 | chr2:17877847-18361616:+ | 0.16 | 0 | 1 | 0 |
| heat shock protein family D (Hsp60) member 1 | ENSG00000144381 | HSPD1 | chr2:197486581-197516737:- | 0.16 | 0 | 1 | 0 |
| par-6 family cell polarity regulator alpha | ENSG00000102981 | PARD6A | chr16:67660946-67662778:+ | 0.16 | 0.31 | 1 | 1 |
| tetratricopeptide repeat domain 17 | ENSG00000052841 | TTC17 | chr11:43358932-43494933:+ | 0.15 | 0 | 1 | 0 |
| neuropeptides B and W receptor 1 | ENSG00000183729 | NPBWR1 | chr8:52938431-52941117:+ | 0.15 | 0 | 1 | 0 |
| G protein-coupled receptor 146 | ENSG00000164849 | GPR146 | chr7:1044576-1059261:+ | 0.15 | 0.4 | 1 | 1 |
| cyclin and CBS domain divalent metal cation transport mediator 4 | ENSG00000158158 | CNNM4 | chr2:96760902-96811891:+ | 0.15 | 0 | 1 | 0 |
| cyclin and CBS domain divalent metal cation transport mediator 3 | ENSG00000168763 | CNNM3 | chr2:96816245-96833911:+ | 0.15 | 0 | 1 | 0 |
| opioid related nociceptin receptor 1 | ENSG00000125510 | OPRL1 | chr20:64080173-64100643:+ | 0.15 | 0 | 1 | 0 |
| EH domain containing 1 | ENSG00000110047 | EHD1 | chr11:64851642-64888296:- | 0.15 | 0 | 1 | 0 |
| adhesion G protein-coupled receptor G2 | ENSG00000173698 | ADGRG2 | chrX:18989309-19122637:- | 0.15 | 0 | 1 | 0 |
| filamin A | ENSG00000196924 | FLNA | chrX:154348524-154374638:- | 0.15 | 0 | 1 | 0 |
| solute carrier family 13 member 3 | ENSG00000158296 | SLC13A3 | chr20:46557823-46684467:- | 0.15 | 0 | 1 | 0 |
| plexin B3 | ENSG00000198753 | PLXNB3 | chrX:153764196-153779346:+ | 0.14 | 0 | 1 | 0 |
| EH domain containing 3 | ENSG00000013016 | EHD3 | chr2:31234337-31269447:+ | 0.14 | 0 | 1 | 0 |
| CASP8 and FADD like apoptosis regulator | ENSG00000003402 | CFLAR | chr2:201116104-201176687:+ | 0.14 | 0 | 1 | 0 |
| family with sequence similarity 126 member B | ENSG00000155744 | FAM126B | chr2:200973718-201071671:- | 0.14 | 0 | 1 | 0 |
| EH domain containing 2 | ENSG00000024422 | EHD2 | chr19:47713343-47743134:+ | 0.14 | 0.44 | 1 | 2 |
| stomatin like 2 | ENSG00000165283 | STOML2 | chr9:35099776-35103195:- | 0.14 | 0 | 1 | 0 |
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