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 |
| OLFM2 | ENSG00000105088 | 0.00 | 0.00 | 0 | 0 |
| PLSCR4 | ENSG00000114698 | 0.00 | 0.00 | 0 | 0 |
| HDAC10 | ENSG00000100429 | 0.00 | 1.30 | 0 | 6 |
| PRKCH | ENSG00000027075 | 0.00 | 0.25 | 0 | 1 |
| NOTCH3 | ENSG00000074181 | 0.23 | 0.00 | 1 | 0 |
| ALOX12 | ENSG00000108839 | 0.00 | 0.00 | 0 | 0 |
| GPR68 | ENSG00000119714 | 0.00 | 0.00 | 0 | 0 |
| NRP1 | ENSG00000099250 | 0.00 | 0.00 | 0 | 0 |
| ABCA13 | ENSG00000179869 | 0.00 | 0.00 | 0 | 0 |
| ADCY3 | ENSG00000138031 | 0.17 | 0.00 | 1 | 0 |
| PBRM1 | ENSG00000163939 | 0.00 | 0.91 | 0 | 5 |
| SPINK5 | ENSG00000133710 | 0.00 | 0.00 | 0 | 0 |
| NTRK1 | ENSG00000198400 | 0.00 | 0.00 | 0 | 0 |
| PRSS1 | ENSG00000204983 | 0.00 | 0.00 | 0 | 0 |
| PPIL6 | ENSG00000185250 | 0.00 | 0.12 | 0 | 1 |
| MAK | ENSG00000111837 | 0.00 | 0.00 | 0 | 0 |
| COL9A2 | ENSG00000049089 | 0.27 | 0.00 | 2 | 0 |
| NCEH1 | ENSG00000144959 | 0.92 | 0.00 | 2 | 0 |
| SFRP5 | ENSG00000120057 | 0.00 | 0.33 | 0 | 1 |
| MTA1 | ENSG00000182979 | 0.58 | 0.45 | 2 | 2 |
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