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 |
| Bardet-Biedl syndrome 2 | ENSG00000125124 | BBS2 | chr16:56466836-56520283:- | 0.12 | 0.12 | 1 | 1 |
| C-X3-C motif chemokine ligand 1 | ENSG00000006210 | CX3CL1 | chr16:57372458-57385048:+ | 0.12 | 0 | 1 | 0 |
| phosphatidylinositol glycan anchor biosynthesis class N | ENSG00000197563 | PIGN | chr18:62043567-62187118:- | 0.11 | 0.55 | 1 | 4 |
| cholinergic receptor muscarinic 3 | ENSG00000133019 | CHRM3 | chr1:239386565-239915452:+ | 0.11 | 0 | 1 | 0 |
| RP2 activator of ARL3 GTPase | ENSG00000102218 | RP2 | chrX:46836940-46882358:+ | 0.11 | 0 | 1 | 0 |
| smoothened, frizzled class receptor | ENSG00000128602 | SMO | chr7:129188872-129213545:+ | 0.11 | 0.14 | 1 | 1 |
| tetraspanin 33 | ENSG00000158457 | TSPAN33 | chr7:129144892-129169697:+ | 0.11 | 0 | 1 | 0 |
| catenin delta 1 | ENSG00000198561 | CTNND1 | chr11:57753243-57819546:+ | 0.11 | 0.11 | 1 | 1 |
| syntaxin 4 | ENSG00000103496 | STX4 | chr16:31032889-31042975:+ | 0.11 | 0 | 1 | 0 |
| erythroblast membrane associated protein (Scianna blood group) | ENSG00000164010 | ERMAP | chr1:42817124-42844989:+ | 0.11 | 0 | 1 | 0 |
| adiponectin receptor 1 | ENSG00000159346 | ADIPOR1 | chr1:202940823-202958572:- | 0.11 | 0 | 1 | 0 |
| tetraspanin 13 | ENSG00000106537 | TSPAN13 | chr7:16753535-16784536:+ | 0.11 | 0 | 1 | 0 |
| solute carrier organic anion transporter family member 4A1 | ENSG00000101187 | SLCO4A1 | chr20:62642445-62685785:+ | 0.11 | 0 | 1 | 0 |
| chromosome 1 open reading frame 210 | ENSG00000253313 | C1orf210 | chr1:43281883-43285617:- | 0.11 | 0 | 1 | 0 |
| transmembrane protein 63A | ENSG00000196187 | TMEM63A | chr1:225845536-225882369:- | 0.11 | 0.24 | 1 | 1 |
| jagged canonical Notch ligand 1 | ENSG00000101384 | JAG1 | chr20:10637684-10674107:- | 0.11 | 0 | 1 | 0 |
| EPH receptor A1 | ENSG00000146904 | EPHA1 | chr7:143390289-143408892:- | 0.11 | 0 | 1 | 0 |
| GRIP and coiled-coil domain containing 1 | ENSG00000179562 | GCC1 | chr7:127580618-127593611:- | 0.11 | 0.25 | 1 | 2 |
| dipeptidyl peptidase like 6 | ENSG00000130226 | DPP6 | chr7:153887097-154894285:+ | 0.11 | 0 | 1 | 0 |
| rhomboid like 2 | ENSG00000158315 | RHBDL2 | chr1:38885807-38941799:- | 0.11 | 0 | 1 | 0 |
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