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 |
| ATAD2B | ENSG00000119778 | 0.17 | 0.13 | 1 | 1 |
| ABCG1 | ENSG00000160179 | 0.00 | 0.00 | 0 | 0 |
| KCNJ5 | ENSG00000120457 | 0.00 | 0.19 | 0 | 1 |
| HRH2 | ENSG00000113749 | 0.33 | 0.11 | 1 | 1 |
| ABCC6 | ENSG00000091262 | 0.00 | 0.00 | 0 | 0 |
| GABRP | ENSG00000094755 | 0.00 | 0.00 | 0 | 0 |
| NTF3 | ENSG00000185652 | 0.58 | 0.00 | 1 | 0 |
| IL1RAP | ENSG00000196083 | 0.39 | 0.00 | 2 | 0 |
| NAALAD2 | ENSG00000077616 | 0.00 | 0.00 | 0 | 0 |
| TYK2 | ENSG00000105397 | 0.00 | 0.00 | 0 | 0 |
| TUBD1 | ENSG00000108423 | 1.00 | 0.00 | 5 | 0 |
| CHRD | ENSG00000090539 | 0.22 | 0.00 | 1 | 0 |
| PTGER1 | ENSG00000160951 | 0.00 | 0.00 | 0 | 0 |
| HLA-B | ENSG00000234745 | 0.00 | 0.00 | 0 | 0 |
| LGALS3BP | ENSG00000108679 | 0.46 | 0.00 | 2 | 0 |
| HSP90AA1 | ENSG00000080824 | 0.17 | 0.31 | 1 | 1 |
| HDAC7 | ENSG00000061273 | 0.16 | 0.00 | 1 | 0 |
| SPOCK1 | ENSG00000152377 | 0.00 | 0.00 | 0 | 0 |
| CAMK2A | ENSG00000070808 | 0.00 | 0.00 | 0 | 0 |
| NCAN | ENSG00000130287 | 0.00 | 0.00 | 0 | 0 |
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