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 |
| C-type lectin domain containing 5A | ENSG00000258227 | CLEC5A | chr7:141927357-141947007:- | 0.1 | 0 | 1 | 0 |
| potassium voltage-gated channel subfamily H member 2 | ENSG00000055118 | KCNH2 | chr7:150944961-150978315:- | 0.1 | 0 | 1 | 0 |
| solute carrier family 19 member 1 | ENSG00000173638 | SLC19A1 | chr21:45493572-45544411:- | 0.1 | 0.18 | 1 | 1 |
| proline rich 7, synaptic | ENSG00000131188 | PRR7 | chr5:177446445-177456286:+ | 0.1 | 0 | 1 | 0 |
| chondroitin polymerizing factor 2 | ENSG00000033100 | CHPF2 | chr7:151232489-151238827:+ | 0.1 | 0.23 | 1 | 1 |
| serine protease 8 | ENSG00000052344 | PRSS8 | chr16:31131433-31135762:- | 0.1 | 0 | 1 | 0 |
| myelin protein zero | ENSG00000158887 | MPZ | chr1:161304735-161309972:- | 0.1 | 0 | 1 | 0 |
| solute carrier family 4 member 2 | ENSG00000164889 | SLC4A2 | chr7:151057210-151076527:+ | 0.1 | 0.19 | 1 | 1 |
| cyclin dependent kinase 5 | ENSG00000164885 | CDK5 | chr7:151053812-151058530:- | 0.1 | 0.19 | 1 | 1 |
| thioredoxin related transmembrane protein 3 | ENSG00000166479 | TMX3 | chr18:68673688-68715298:- | 0.1 | 0.56 | 1 | 4 |
| solute carrier family 9 member A7 | ENSG00000065923 | SLC9A7 | chrX:46599252-46759172:- | 0.1 | 0 | 1 | 0 |
| calsyntenin 1 | ENSG00000171603 | CLSTN1 | chr1:9729026-9824526:- | 0 | 2.06 | 0 | 6 |
| chloride voltage-gated channel 6 | ENSG00000011021 | CLCN6 | chr1:11806096-11843144:+ | 0 | 2.01 | 0 | 6 |
| cell division cycle 42 | ENSG00000070831 | CDC42 | chr1:22052627-22092946:+ | 0 | 1.94 | 0 | 6 |
| endothelin converting enzyme 1 | ENSG00000117298 | ECE1 | chr1:21217247-21345504:- | 0 | 1.84 | 0 | 5 |
| glypican 1 | ENSG00000063660 | GPC1 | chr2:240435671-240468078:+ | 0 | 1.72 | 0 | 8 |
| anoctamin 7 | ENSG00000146205 | ANO7 | chr2:241188509-241225377:+ | 0 | 1.64 | 0 | 7 |
| XK related 8 | ENSG00000158156 | XKR8 | chr1:27959462-27968096:+ | 0 | 1.63 | 0 | 4 |
| lysophosphatidic acid receptor 6 | ENSG00000139679 | LPAR6 | chr13:48389567-48444704:- | 0 | 1.63 | 0 | 5 |
| G protein subunit beta 1 | ENSG00000078369 | GNB1 | chr1:1785285-1891117:- | 0 | 1.62 | 0 | 8 |
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