Copy Number
The putative cancer-associated PDGs 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 Symbol | Ensembl Gene ID | Amplification | Deletion | Amplification | Deletion |
| CALU | ENSG00000128595 | 0.11 | 0.00 | 1 | 0 |
| LRRC17 | ENSG00000128606 | 0.00 | 0.00 | 0 | 0 |
| OPN1SW | ENSG00000128617 | 0.00 | 0.00 | 0 | 0 |
| TWSG1 | ENSG00000128791 | 0.00 | 0.00 | 0 | 0 |
| DLL4 | ENSG00000128917 | 0.00 | 0.11 | 0 | 1 |
| DUT | ENSG00000128951 | 0.00 | 0.00 | 0 | 0 |
| ACKR4 | ENSG00000129048 | 0.00 | 0.00 | 0 | 0 |
| PSMA1 | ENSG00000129084 | 0.00 | 0.00 | 0 | 0 |
| SPCS3 | ENSG00000129128 | 0.00 | 0.45 | 0 | 3 |
| USP6 | ENSG00000129204 | 0.00 | 0.00 | 0 | 0 |
| SHBG | ENSG00000129214 | 0.00 | 0.00 | 0 | 0 |
| AIPL1 | ENSG00000129221 | 0.00 | 0.00 | 0 | 0 |
| CD68 | ENSG00000129226 | 0.00 | 0.16 | 0 | 1 |
| PHF20L1 | ENSG00000129292 | 1.46 | 0.00 | 5 | 0 |
| KLK14 | ENSG00000129437 | 0.00 | 0.00 | 0 | 0 |
| SIGLEC9 | ENSG00000129450 | 0.00 | 0.00 | 0 | 0 |
| KLK10 | ENSG00000129451 | 0.23 | 0.00 | 1 | 0 |
| KLK8 | ENSG00000129455 | 0.00 | 0.00 | 0 | 0 |
| RIPK3 | ENSG00000129465 | 0.00 | 0.00 | 0 | 0 |
| BCL2L2 | ENSG00000129473 | 0.28 | 0.00 | 1 | 0 |
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