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 |
| SP100 | ENSG00000067066 | 0 | 1.22 | 0 | 5 |
| SP110 | ENSG00000135899 | 0 | 1.19 | 0 | 5 |
| TRIM28 | ENSG00000130726 | 0.14 | 0.3 | 1 | 1 |
| TRIM33 | ENSG00000197323 | 0 | 0.66 | 0 | 4 |
| TRIM24 | ENSG00000122779 | 0.33 | 0.14 | 2 | 1 |
| TRIM66 | ENSG00000166436 | 0 | 0 | 0 | 0 |
| BAZ1A | ENSG00000198604 | 0 | 0 | 0 | 0 |
| SMARCA2 | ENSG00000080503 | 0.13 | 0 | 1 | 0 |
| SMARCA4 | ENSG00000127616 | 0 | 0 | 0 | 0 |
| ASH1L | ENSG00000116539 | 1.11 | 0 | 4 | 0 |
| BAZ1B | ENSG00000009954 | 0.12 | 0 | 1 | 0 |
| PBRM1 | ENSG00000163939 | 0 | 0.91 | 0 | 5 |
| ZMYND8 | ENSG00000101040 | 0.33 | 0 | 2 | 0 |
| ZMYND11 | ENSG00000015171 | 0 | 0.65 | 0 | 3 |
| BRD4 | ENSG00000141867 | 2.08 | 0 | 6 | 0 |
| BPTF | ENSG00000171634 | 0.99 | 0 | 5 | 0 |
| BRD2 | ENSG00000204256 | 0 | 0 | 0 | 0 |
| BRDT | ENSG00000137948 | 0 | 0 | 0 | 0 |
| BRD3 | ENSG00000169925 | 0 | 0.25 | 0 | 1 |
| KMT2A | ENSG00000118058 | 0 | 0.64 | 0 | 3 |
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