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 |
| MGEA5 | ENSG00000198408 | 0.00 | 0.48 | 0 | 2 |
| CHID1 | ENSG00000177830 | 0.00 | 0.57 | 0 | 4 |
| A1BG | ENSG00000121410 | 0.00 | 0.35 | 0 | 1 |
| ATRN | ENSG00000088812 | 0.39 | 0.00 | 2 | 0 |
| PKN1 | ENSG00000123143 | 0.26 | 0.00 | 1 | 0 |
| NRD1 | ENSG00000078618 | 0.00 | 0.00 | 0 | 0 |
| ENTPD1 | ENSG00000138185 | 0.00 | 0.00 | 0 | 0 |
| CAPNS1 | ENSG00000126247 | 0.00 | 0.00 | 0 | 0 |
| ADCY6 | ENSG00000174233 | 0.00 | 0.00 | 0 | 0 |
| ATP4A | ENSG00000105675 | 0.00 | 0.00 | 0 | 0 |
| TRAP1 | ENSG00000126602 | 0.00 | 0.00 | 0 | 0 |
| SLC30A5 | ENSG00000145740 | 0.00 | 1.23 | 0 | 4 |
| KDM4A | ENSG00000066135 | 0.00 | 0.00 | 0 | 0 |
| PARP14 | ENSG00000173193 | 0.00 | 0.00 | 0 | 0 |
| PSAP | ENSG00000197746 | 0.00 | 0.00 | 0 | 0 |
| CELA2A | ENSG00000142615 | 0.00 | 0.00 | 0 | 0 |
| RHAG | ENSG00000112077 | 0.00 | 0.00 | 0 | 0 |
| SLC30A6 | ENSG00000152683 | 0.13 | 0.00 | 1 | 0 |
| HAT1 | ENSG00000128708 | 0.00 | 0.00 | 0 | 0 |
| RIOK3 | ENSG00000101782 | 0.13 | 0.00 | 1 | 0 |
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