Copy Number
The putative cancer-causing HAMPs 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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| HGNC | Ensembl | Overall_Gscore | No. of Cancer Types | ||
| Symbol | Gene ID | Amplification | Deletion | Amplification | Deletion |
| HDAC10 | ENSG00000100429 | 0 | 1.3 | 0 | 6 |
| HDAC6 | ENSG00000094631 | 0 | 0 | 0 | 0 |
| HDAC7 | ENSG00000061273 | 0.16 | 0 | 1 | 0 |
| HDAC4 | ENSG00000068024 | 0 | 1.97 | 0 | 8 |
| HDAC5 | ENSG00000108840 | 0 | 0.5 | 0 | 3 |
| HDAC9 | ENSG00000048052 | 0.11 | 0 | 1 | 0 |
| SIRT6 | ENSG00000077463 | 0 | 0.74 | 0 | 1 |
| SIRT3 | ENSG00000142082 | 0 | 1.32 | 0 | 6 |
| SIRT1 | ENSG00000096717 | 0 | 0 | 0 | 0 |
| SIRT2 | ENSG00000068903 | 0 | 0 | 0 | 0 |
| SIRT7 | ENSG00000187531 | 0.45 | 0 | 2 | 0 |
| SIRT4 | ENSG00000089163 | 0 | 0.17 | 0 | 1 |
| SIRT5 | ENSG00000124523 | 0.67 | 0.13 | 3 | 1 |
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