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 |
| TYRO3 | ENSG00000092445 | 0.00 | 1.16 | 0 | 5 |
| SNAP23 | ENSG00000092531 | 0.00 | 0.62 | 0 | 3 |
| TGFB2 | ENSG00000092969 | 0.00 | 0.14 | 0 | 1 |
| COMT | ENSG00000093010 | 0.17 | 0.00 | 1 | 0 |
| CECR1 | ENSG00000093072 | 0.00 | 0.00 | 0 | 0 |
| HDAC6 | ENSG00000094631 | 0.00 | 0.00 | 0 | 0 |
| OR1I1 | ENSG00000094661 | 0.00 | 0.00 | 0 | 0 |
| NXPE1 | ENSG00000095110 | 0.00 | 0.00 | 0 | 0 |
| CYP26A1 | ENSG00000095596 | 0.00 | 0.32 | 0 | 1 |
| TDRD1 | ENSG00000095627 | 0.00 | 0.00 | 0 | 0 |
| IL11 | ENSG00000095752 | 0.17 | 0.00 | 1 | 0 |
| MYO3A | ENSG00000095777 | 0.00 | 0.00 | 0 | 0 |
| TPSD1 | ENSG00000095917 | 0.00 | 0.00 | 0 | 0 |
| KCNK16 | ENSG00000095981 | 0.00 | 0.00 | 0 | 0 |
| NCR2 | ENSG00000096264 | 0.00 | 0.00 | 0 | 0 |
| MLN | ENSG00000096395 | 0.00 | 0.00 | 0 | 0 |
| CDC7 | ENSG00000097046 | 0.00 | 0.23 | 0 | 2 |
| TMED1 | ENSG00000099203 | 0.00 | 0.00 | 0 | 0 |
| PRTFDC1 | ENSG00000099256 | 0.00 | 0.00 | 0 | 0 |
| KCNK6 | ENSG00000099337 | 0.86 | 0.00 | 2 | 0 |
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