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 |
| USP4 | ENSG00000114316 | 0.00 | 1.11 | 0 | 6 |
| MFSD1 | ENSG00000118855 | 0.00 | 0.00 | 0 | 0 |
| SLC25A25 | ENSG00000148339 | 0.00 | 0.11 | 0 | 1 |
| CXCR4 | ENSG00000121966 | 0.00 | 0.00 | 0 | 0 |
| BDNF | ENSG00000176697 | 0.00 | 0.12 | 0 | 1 |
| SLC6A8 | ENSG00000130821 | 0.00 | 0.00 | 0 | 0 |
| KDM4B | ENSG00000127663 | 0.00 | 0.00 | 0 | 0 |
| WARS2 | ENSG00000116874 | 0.00 | 0.30 | 0 | 2 |
| SRPK2 | ENSG00000135250 | 0.00 | 0.00 | 0 | 0 |
| TXNRD2 | ENSG00000184470 | 0.30 | 0.00 | 2 | 0 |
| PHF2 | ENSG00000197724 | 0.00 | 0.00 | 0 | 0 |
| PARP4 | ENSG00000102699 | 0.00 | 0.17 | 0 | 1 |
| DECR1 | ENSG00000104325 | 0.49 | 0.00 | 2 | 0 |
| AGBL5 | ENSG00000084693 | 0.17 | 0.00 | 1 | 0 |
| MKNK2 | ENSG00000099875 | 0.00 | 0.94 | 0 | 2 |
| SLC44A2 | ENSG00000129353 | 0.83 | 0.00 | 1 | 0 |
| DHRS7 | ENSG00000100612 | 0.00 | 0.23 | 0 | 1 |
| EIF2AK2 | ENSG00000055332 | 0.00 | 0.00 | 0 | 0 |
| SLCO1B1 | ENSG00000134538 | 0.00 | 0.00 | 0 | 0 |
| BAZ1B | ENSG00000009954 | 0.12 | 0.00 | 1 | 0 |
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