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 |
| proton activated chloride channel 1 | ENSG00000065600 | TMEM206 | chr1:212363931-212414901:- | 0 | 0.17 | 0 | 1 |
| calcium voltage-gated channel subunit alpha1 D | ENSG00000157388 | CACNA1D | chr3:53494656-53813733:+ | 0 | 0.16 | 0 | 1 |
| lymphocyte specific protein 1 | ENSG00000130592 | LSP1 | chr11:1852970-1892267:+ | 0 | 0.16 | 0 | 1 |
| solute carrier family 22 member 18 | ENSG00000110628 | SLC22A18 | chr11:2899721-2925246:+ | 0 | 0.16 | 0 | 1 |
| CD68 molecule | ENSG00000129226 | CD68 | chr17:7579467-7582113:+ | 0 | 0.16 | 0 | 1 |
| cyclase associated actin cytoskeleton regulatory protein 2 | ENSG00000112186 | CAP2 | chr6:17393216-17557792:+ | 0 | 0.16 | 0 | 1 |
| family with sequence similarity 234 member B | ENSG00000084444 | KIAA1467 | chr12:13044284-13142521:+ | 0 | 0.16 | 0 | 1 |
| TNF superfamily member 12 | ENSG00000239697 | TNFSF12 | chr17:7548891-7557890:+ | 0 | 0.16 | 0 | 1 |
| potassium two pore domain channel subfamily K member 2 | ENSG00000082482 | KCNK2 | chr1:215005775-215237093:+ | 0 | 0.16 | 0 | 1 |
| ATP binding cassette subfamily B member 9 | ENSG00000150967 | ABCB9 | chr12:122920951-122981649:- | 0 | 0.16 | 0 | 1 |
| golgi membrane protein 1 | ENSG00000135052 | GOLM1 | chr9:86026146-86100173:- | 0 | 0.15 | 0 | 1 |
| G protein subunit alpha q | ENSG00000156052 | GNAQ | chr9:77716087-78031458:- | 0 | 0.15 | 0 | 1 |
| neuroligin 2 | ENSG00000169992 | NLGN2 | chr17:7404874-7419860:+ | 0 | 0.15 | 0 | 1 |
| cholinergic receptor nicotinic beta 1 subunit | ENSG00000170175 | CHRNB1 | chr17:7445061-7457707:+ | 0 | 0.15 | 0 | 1 |
| phospholipid scramblase 3 | ENSG00000187838 | TMEM256-PLSCR3 | chr17:7389727-7394843:- | 0 | 0.15 | 0 | 1 |
| gap junction protein alpha 1 | ENSG00000152661 | GJA1 | chr6:121435692-121449727:+ | 0 | 0.15 | 0 | 1 |
| solute carrier family 31 member 1 | ENSG00000136868 | SLC31A1 | chr9:113221562-113264492:+ | 0 | 0.15 | 0 | 1 |
| ATP binding cassette subfamily A member 7 | ENSG00000064687 | ABCA7 | chr19:1040101-1065572:+ | 0 | 0.15 | 0 | 1 |
| LHFPL tetraspan subfamily member 2 | ENSG00000145685 | LHFPL2 | chr5:78485215-78770021:- | 0 | 0.15 | 0 | 1 |
| protocadherin 1 | ENSG00000156453 | PCDH1 | chr5:141853111-141879246:- | 0 | 0.15 | 0 | 1 |
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