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 |
| NCK associated protein 1 | ENSG00000061676 | NCKAP1 | chr2:182909115-183038858:- | 0.12 | 0 | 1 | 0 |
| syntaxin 1A | ENSG00000106089 | STX1A | chr7:73699206-73719672:- | 0.12 | 0 | 1 | 0 |
| KIAA1549 | ENSG00000122778 | KIAA1549 | chr7:138831381-138981318:- | 0.12 | 0 | 1 | 0 |
| kinase insert domain receptor | ENSG00000128052 | KDR | chr4:55078477-55125589:- | 0.12 | 0 | 1 | 0 |
| ribitol xylosyltransferase 1 | ENSG00000118600 | TMEM5 | chr12:63779803-63809558:+ | 0.12 | 0 | 1 | 0 |
| retinal outer segment membrane protein 1 | ENSG00000149489 | ROM1 | chr11:62611722-62615120:+ | 0.12 | 0.12 | 1 | 1 |
| CD46 molecule | ENSG00000117335 | CD46 | chr1:207752057-207795513:+ | 0.12 | 0 | 1 | 0 |
| plexin A2 | ENSG00000076356 | PLXNA2 | chr1:208022242-208244320:- | 0.12 | 0 | 1 | 0 |
| G protein-coupled receptor 155 | ENSG00000163328 | GPR155 | chr2:174431571-174487094:- | 0.12 | 0 | 1 | 0 |
| microtubule affinity regulating kinase 2 | ENSG00000072518 | MARK2 | chr11:63838928-63911019:+ | 0.12 | 0.16 | 1 | 1 |
| solute carrier family 41 member 1 | ENSG00000133065 | SLC41A1 | chr1:205789093-205813748:- | 0.12 | 0 | 1 | 0 |
| ADP ribosylation factor 6 | ENSG00000165527 | ARF6 | chr14:49893092-49897054:+ | 0.12 | 0 | 1 | 0 |
| beta-secretase 2 | ENSG00000182240 | BACE2 | chr21:41167801-41282518:+ | 0.12 | 0.16 | 1 | 1 |
| CD276 molecule | ENSG00000103855 | CD276 | chr15:73683966-73714518:+ | 0.12 | 0 | 1 | 0 |
| solute carrier family 3 member 1 | ENSG00000138079 | SLC3A1 | chr2:44275458-44321494:+ | 0.12 | 0 | 1 | 0 |
| beta-1,4-galactosyltransferase 5 | ENSG00000158470 | B4GALT5 | chr20:49632945-49713878:- | 0.12 | 0 | 1 | 0 |
| proline rich transmembrane protein 4 | ENSG00000224940 | PRRT4 | chr7:128350325-128361685:- | 0.12 | 0 | 1 | 0 |
| sulfatase 2 | ENSG00000196562 | SULF2 | chr20:47656348-47786616:- | 0.12 | 0 | 1 | 0 |
| solute carrier family 38 member 7 | ENSG00000103042 | SLC38A7 | chr16:58665109-58685104:- | 0.12 | 0.16 | 1 | 1 |
| glutamic-oxaloacetic transaminase 2 | ENSG00000125166 | GOT2 | chr16:58707131-58734357:- | 0.12 | 0.16 | 1 | 1 |
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