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 organic anion transporter family member 3A1 | ENSG00000176463 | SLCO3A1 | chr15:91853695-92172435:+ | 0.18 | 0 | 1 | 0 |
| FES proto-oncogene, tyrosine kinase | ENSG00000182511 | FES | chr15:90883695-90895776:+ | 0.18 | 0 | 1 | 0 |
| pecanex 3 | ENSG00000197136 | PCNXL3 | chr11:65615773-65637439:+ | 0.18 | 0 | 1 | 0 |
| proline rich and Gla domain 1 | ENSG00000130962 | PRRG1 | chrX:37349275-37457295:+ | 0.18 | 0 | 1 | 0 |
| YES proto-oncogene 1, Src family tyrosine kinase | ENSG00000176105 | YES1 | chr18:721588-812546:- | 0.18 | 0.12 | 1 | 1 |
| transient receptor potential cation channel subfamily A member 1 | ENSG00000104321 | TRPA1 | chr8:72019917-72075617:- | 0.18 | 0 | 1 | 0 |
| myogenesis regulating glycosidase (putative) | ENSG00000164976 | KIAA1161 | chr9:34366670-34376853:- | 0.18 | 0 | 1 | 0 |
| reticulon 4 receptor | ENSG00000040608 | RTN4R | chr22:20241415-20283246:- | 0.17 | 0 | 1 | 0 |
| seizure related 6 homolog like 2 | ENSG00000174938 | SEZ6L2 | chr16:29871159-29899547:- | 0.17 | 0 | 1 | 0 |
| transmembrane protein 219 | ENSG00000149932 | TMEM219 | chr16:29940885-29973052:+ | 0.17 | 0 | 1 | 0 |
| dynein cytoplasmic 2 heavy chain 1 | ENSG00000187240 | DYNC2H1 | chr11:103109431-103479863:+ | 0.17 | 0.46 | 1 | 2 |
| proline rich transmembrane protein 2 | ENSG00000167371 | PRRT2 | chr16:29811382-29815892:+ | 0.17 | 0 | 1 | 0 |
| CDP-diacylglycerol--inositol 3-phosphatidyltransferase | ENSG00000103502 | CDIPT | chr16:29858357-29863736:- | 0.17 | 0 | 1 | 0 |
| solute carrier family 22 member 23 | ENSG00000137266 | SLC22A23 | chr6:3268962-3457022:- | 0.17 | 0.14 | 1 | 1 |
| ATPase 13A3 | ENSG00000133657 | ATP13A3 | chr3:194402672-194498364:- | 0.17 | 0.11 | 1 | 1 |
| glutamate ionotropic receptor NMDA type subunit 1 | ENSG00000176884 | GRIN1 | chr9:137138390-137168762:+ | 0.17 | 0 | 1 | 0 |
| leucine rich repeat containing 37 member A3 | ENSG00000176809 | LRRC37A3 | chr17:64854312-64919480:- | 0.17 | 0 | 1 | 0 |
| ADAM metallopeptidase domain 17 | ENSG00000151694 | ADAM17 | chr2:9488486-9555792:- | 0.17 | 0.16 | 1 | 1 |
| amnion associated transmembrane protein | ENSG00000166126 | AMN | chr14:102922656-102933596:+ | 0.17 | 0 | 1 | 0 |
| cadherin 3 | ENSG00000062038 | CDH3 | chr16:68636189-68722616:+ | 0.17 | 0.35 | 1 | 1 |
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