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 |
| KAT6A | ENSG00000083168 | 1.74 | 0 | 6 | 0 |
| KAT6B | ENSG00000156650 | 0.65 | 0 | 1 | 0 |
| KAT7 | ENSG00000136504 | 0 | 0 | 0 | 0 |
| KAT5 | ENSG00000172977 | 0.18 | 0 | 1 | 0 |
| KAT8 | ENSG00000103510 | 0.1 | 0 | 1 | 0 |
| CLOCK | ENSG00000134852 | 1.29 | 0 | 5 | 0 |
| HAT1 | ENSG00000128708 | 0 | 0 | 0 | 0 |
| ELP3 | ENSG00000134014 | 0 | 0.28 | 0 | 2 |
| KAT2A | ENSG00000108773 | 0 | 0.2 | 0 | 1 |
| KAT2B | ENSG00000114166 | 0 | 0.17 | 0 | 1 |
| TAF1 | ENSG00000147133 | 0 | 0 | 0 | 0 |
| TAF1L | ENSG00000122728 | 0 | 0 | 0 | 0 |
| ATAT1 | ENSG00000137343 | 0.2 | 0 | 1 | 0 |
| CREBBP | ENSG00000005339 | 0 | 0.33 | 0 | 2 |
| EP300 | ENSG00000100393 | 0.33 | 0 | 1 | 0 |
| GTF3C4 | ENSG00000125484 | 0 | 0.39 | 0 | 2 |
| NCOA1 | ENSG00000084676 | 0 | 0 | 0 | 0 |
| NCOA3 | ENSG00000124151 | 0.12 | 0 | 1 | 0 |
| SP140 | ENSG00000079263 | 0 | 0.69 | 0 | 3 |
| SP140L | ENSG00000185404 | 0 | 1.2 | 0 | 5 |
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