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 |
| ATG4B | ENSG00000168397 | 0.00 | 2.47 | 0 | 10 |
| SFTPD | ENSG00000133661 | 0.00 | 0.00 | 0 | 0 |
| ROR2 | ENSG00000169071 | 0.00 | 0.00 | 0 | 0 |
| ABCC1 | ENSG00000103222 | 0.00 | 0.00 | 0 | 0 |
| PHEX | ENSG00000102174 | 0.00 | 0.00 | 0 | 0 |
| CPD | ENSG00000108582 | 0.00 | 0.00 | 0 | 0 |
| CHRNA9 | ENSG00000174343 | 0.00 | 0.00 | 0 | 0 |
| ITGA5 | ENSG00000161638 | 0.00 | 0.00 | 0 | 0 |
| CYP2S1 | ENSG00000167600 | 0.00 | 0.00 | 0 | 0 |
| PRKAR1B | ENSG00000188191 | 0.54 | 0.41 | 4 | 1 |
| AMPD3 | ENSG00000133805 | 0.00 | 0.00 | 0 | 0 |
| ADAMTS6 | ENSG00000049192 | 0.00 | 0.00 | 0 | 0 |
| SLC9B2 | ENSG00000164038 | 0.00 | 0.13 | 0 | 1 |
| GANC | ENSG00000214013 | 0.00 | 0.84 | 0 | 5 |
| CARD17 | ENSG00000255221 | 0.00 | 0.00 | 0 | 0 |
| PLA1A | ENSG00000144837 | 0.00 | 0.00 | 0 | 0 |
| ACACA | ENSG00000278540 | 0.00 | 0.00 | 0 | 0 |
| CDC14B | ENSG00000081377 | 0.00 | 0.00 | 0 | 0 |
| SLC47A2 | ENSG00000180638 | 0.00 | 0.00 | 0 | 0 |
| AQP9 | ENSG00000103569 | 0.00 | 0.00 | 0 | 0 |
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