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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| KIRC | KIRP | KICH | PRAD | BLCA | THYM | MESO | LUAD | LUSC | HNSC | ESCA | STAD | COAD | READ | PAAD | LIHC | CHOL | ACC | PCPG | THCA | BRCA | OV | CESC | UCEC | UCS | SARC | TGCT | LAML | DLBC | LGG | GBM | UVM | SKCM | |||||||||||||||||||||||||||||||||||
| HGNC Symbol | Ensembl Gene ID | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del |
| USP4 | ENSG00000114316 | 0.00 | 0.18 | 0.00 | 0.02 | 0.05 | 0.00 | 0.00 | 0.02 | 0.03 | 0.15 | 0.00 | 0.01 | 0.00 | 0.54 | 0.01 | 0.06 | 0.00 | 0.10 | 0.00 | 0.06 | 0.01 | 0.13 | 0.01 | 0.11 | 0.00 | 0.05 | 0.02 | 0.09 | 0.00 | 0.04 | 0.05 | 0.05 | 0.00 | 0.24 | 0.06 | 0.03 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.17 | 0.07 | 0.20 | 0.00 | 0.06 | 0.06 | 0.05 | 0.06 | 0.30 | 0.02 | 0.17 | 0.02 | 0.03 | 0.00 | 0.01 | 0.00 | 0.16 | 0.00 | 0.05 | 0.02 | 0.04 | 0.00 | 0.03 | 0.01 | 0.04 |
| MFSD1 | ENSG00000118855 | 0.04 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.04 | 0.01 | 0.11 | 0.01 | 0.00 | 0.00 | 0.00 | 0.04 | 0.12 | 0.01 | 1.02 | 0.00 | 0.47 | 0.00 | 0.66 | 0.01 | 0.17 | 0.00 | 0.02 | 0.00 | 0.05 | 0.01 | 0.03 | 0.00 | 0.08 | 0.01 | 0.03 | 0.01 | 0.10 | 0.01 | 0.00 | 0.06 | 0.00 | 0.00 | 0.15 | 0.01 | 0.75 | 0.02 | 0.49 | 0.01 | 0.18 | 0.01 | 0.21 | 0.02 | 0.07 | 0.07 | 0.12 | 0.00 | 0.00 | 0.00 | 0.04 | 0.00 | 0.01 | 0.02 | 0.02 | 0.03 | 0.00 | 0.00 | 0.01 | 0.03 |
| SLC25A25 | ENSG00000148339 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.05 | 0.00 | 0.03 | 0.02 | 0.00 | 0.01 | 0.00 | 0.02 | 0.04 | 0.03 | 0.05 | 0.03 | 0.07 | 0.01 | 0.13 | 0.02 | 0.13 | 0.02 | 0.01 | 0.01 | 0.04 | 0.03 | 0.00 | 0.01 | 0.05 | 0.04 | 0.07 | 0.04 | 0.18 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.07 | 0.04 | 0.11 | 0.18 | 0.05 | 0.01 | 0.08 | 0.05 | 0.23 | 0.11 | 0.04 | 0.08 | 0.02 | 0.04 | 0.01 | 0.00 | 0.05 | 0.00 | 0.02 | 0.00 | 0.03 | 0.02 | 0.00 | 0.00 | 0.04 | 0.02 |
| CXCR4 | ENSG00000121966 | 0.01 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.18 | 0.03 | 0.04 | 0.00 | 0.01 | 0.00 | 0.01 | 0.02 | 0.02 | 0.07 | 0.04 | 0.03 | 0.01 | 0.07 | 0.07 | 0.03 | 0.06 | 0.00 | 0.02 | 0.01 | 0.01 | 0.01 | 0.01 | 0.01 | 0.04 | 0.05 | 0.03 | 0.05 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.06 | 0.11 | 0.14 | 0.02 | 0.02 | 0.04 | 0.01 | 0.07 | 0.00 | 0.13 | 0.04 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.13 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 |
| BDNF | ENSG00000176697 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.05 | 0.06 | 0.00 | 0.00 | 0.00 | 0.04 | 0.06 | 0.02 | 0.05 | 0.03 | 0.02 | 0.03 | 0.14 | 0.04 | 0.06 | 0.03 | 0.03 | 0.01 | 0.00 | 0.02 | 0.01 | 0.02 | 0.02 | 0.00 | 0.00 | 0.01 | 0.02 | 0.05 | 0.02 | 0.04 | 0.00 | 0.00 | 0.06 | 0.03 | 0.12 | 0.12 | 0.00 | 0.04 | 0.04 | 0.03 | 0.10 | 0.12 | 0.05 | 0.08 | 0.01 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.02 | 0.01 | 0.00 | 0.00 | 0.01 | 0.01 |
| SLC6A8 | ENSG00000130821 | 0.03 | 0.01 | 0.02 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.12 | 0.04 | 0.06 | 0.00 | 0.06 | 0.01 | 0.22 | 0.01 | 0.18 | 0.02 | 0.14 | 0.01 | 0.24 | 0.01 | 0.17 | 0.02 | 0.05 | 0.01 | 0.10 | 0.01 | 0.07 | 0.00 | 0.12 | 0.03 | 0.10 | 0.01 | 0.14 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.10 | 0.03 | 0.44 | 0.09 | 0.22 | 0.02 | 0.12 | 0.03 | 0.09 | 0.07 | 0.24 | 0.07 | 0.01 | 0.02 | 0.00 | 0.00 | 0.15 | 0.07 | 0.02 | 0.03 | 0.03 | 0.02 | 0.05 | 0.00 | 0.06 | 0.01 |
| KDM4B | ENSG00000127663 | 0.00 | 0.01 | 0.00 | 0.02 | 0.00 | 0.04 | 0.01 | 0.03 | 0.04 | 0.10 | 0.00 | 0.01 | 0.01 | 0.10 | 0.01 | 0.07 | 0.06 | 0.10 | 0.04 | 0.11 | 0.06 | 0.12 | 0.01 | 0.08 | 0.01 | 0.05 | 0.06 | 0.09 | 0.00 | 0.06 | 0.03 | 0.13 | 0.00 | 0.03 | 0.05 | 0.03 | 0.05 | 0.00 | 0.00 | 0.01 | 0.06 | 0.09 | 0.12 | 0.67 | 0.03 | 0.17 | 0.03 | 0.23 | 0.07 | 0.58 | 0.22 | 0.07 | 0.02 | 0.00 | 0.04 | 0.00 | 0.00 | 0.07 | 0.00 | 0.01 | 0.06 | 0.01 | 0.00 | 0.05 | 0.04 | 0.04 |
| WARS2 | ENSG00000116874 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.03 | 0.03 | 0.17 | 0.03 | 0.00 | 0.00 | 0.00 | 0.18 | 0.03 | 0.14 | 0.09 | 0.16 | 0.06 | 0.16 | 0.15 | 0.11 | 0.05 | 0.06 | 0.02 | 0.05 | 0.05 | 0.06 | 0.14 | 0.01 | 0.02 | 0.04 | 0.01 | 0.08 | 0.08 | 0.05 | 0.04 | 0.25 | 0.00 | 0.00 | 0.11 | 0.06 | 0.23 | 0.10 | 0.03 | 0.07 | 0.03 | 0.02 | 0.10 | 0.06 | 0.10 | 0.13 | 0.05 | 0.03 | 0.00 | 0.00 | 0.03 | 0.05 | 0.00 | 0.01 | 0.00 | 0.04 | 0.00 | 0.05 | 0.24 | 0.06 |
| SRPK2 | ENSG00000135250 | 0.01 | 0.00 | 0.05 | 0.01 | 0.01 | 0.00 | 0.03 | 0.02 | 0.03 | 0.02 | 0.00 | 0.00 | 0.03 | 0.00 | 0.08 | 0.02 | 0.18 | 0.03 | 0.17 | 0.02 | 0.41 | 0.07 | 0.17 | 0.04 | 0.02 | 0.01 | 0.03 | 0.00 | 0.02 | 0.02 | 0.05 | 0.03 | 0.00 | 0.02 | 0.02 | 0.06 | 0.00 | 0.02 | 0.00 | 0.00 | 0.06 | 0.05 | 0.29 | 0.07 | 0.05 | 0.03 | 0.05 | 0.05 | 0.30 | 0.05 | 0.16 | 0.03 | 0.08 | 0.01 | 0.00 | 0.00 | 0.13 | 0.03 | 0.09 | 0.00 | 0.02 | 0.01 | 0.00 | 0.00 | 0.08 | 0.04 |
| TXNRD2 | ENSG00000184470 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.05 | 0.17 | 0.06 | 0.03 | 0.01 | 0.08 | 0.05 | 0.07 | 0.03 | 0.17 | 0.07 | 0.10 | 0.03 | 0.08 | 0.07 | 0.05 | 0.04 | 0.02 | 0.01 | 0.06 | 0.03 | 0.00 | 0.02 | 0.02 | 0.03 | 0.08 | 0.10 | 0.10 | 0.14 | 0.01 | 0.01 | 0.02 | 0.00 | 0.06 | 0.05 | 0.19 | 0.07 | 0.05 | 0.01 | 0.06 | 0.06 | 0.42 | 0.04 | 0.14 | 0.07 | 0.13 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 | 0.01 | 0.03 | 0.00 | 0.00 | 0.13 | 0.03 |
| PHF2 | ENSG00000197724 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.03 | 0.01 | 0.06 | 0.05 | 0.00 | 0.01 | 0.01 | 0.04 | 0.01 | 0.05 | 0.04 | 0.02 | 0.04 | 0.00 | 0.10 | 0.01 | 0.02 | 0.04 | 0.01 | 0.01 | 0.04 | 0.03 | 0.00 | 0.01 | 0.01 | 0.03 | 0.00 | 0.08 | 0.04 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.03 | 0.04 | 0.05 | 0.14 | 0.03 | 0.02 | 0.05 | 0.04 | 0.00 | 0.15 | 0.10 | 0.01 | 0.05 | 0.02 | 0.00 | 0.02 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.02 | 0.00 | 0.00 | 0.01 | 0.03 |
| PARP4 | ENSG00000102699 | 0.02 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.05 | 0.09 | 0.06 | 0.00 | 0.02 | 0.00 | 0.17 | 0.02 | 0.11 | 0.02 | 0.12 | 0.01 | 0.15 | 0.10 | 0.09 | 0.08 | 0.04 | 0.22 | 0.00 | 0.22 | 0.02 | 0.01 | 0.00 | 0.03 | 0.12 | 0.00 | 0.15 | 0.00 | 0.09 | 0.00 | 0.00 | 0.00 | 0.01 | 0.10 | 0.08 | 0.11 | 0.18 | 0.04 | 0.14 | 0.02 | 0.04 | 0.02 | 0.16 | 0.12 | 0.19 | 0.00 | 0.01 | 0.00 | 0.00 | 0.04 | 0.09 | 0.00 | 0.06 | 0.01 | 0.06 | 0.00 | 0.00 | 0.05 | 0.04 |
| DECR1 | ENSG00000104325 | 0.00 | 0.01 | 0.01 | 0.01 | 0.06 | 0.03 | 0.09 | 0.02 | 0.23 | 0.01 | 0.02 | 0.00 | 0.02 | 0.01 | 0.14 | 0.02 | 0.14 | 0.03 | 0.07 | 0.01 | 0.20 | 0.01 | 0.14 | 0.01 | 0.10 | 0.00 | 0.16 | 0.00 | 0.03 | 0.01 | 0.17 | 0.00 | 0.20 | 0.01 | 0.06 | 0.00 | 0.03 | 0.01 | 0.00 | 0.00 | 0.35 | 0.00 | 0.35 | 0.10 | 0.07 | 0.01 | 0.07 | 0.01 | 0.45 | 0.02 | 0.16 | 0.06 | 0.15 | 0.00 | 0.00 | 0.00 | 0.04 | 0.04 | 0.05 | 0.01 | 0.01 | 0.01 | 0.33 | 0.00 | 0.09 | 0.01 |
| AGBL5 | ENSG00000084693 | 0.00 | 0.00 | 0.04 | 0.02 | 0.00 | 0.00 | 0.01 | 0.01 | 0.09 | 0.01 | 0.00 | 0.00 | 0.03 | 0.07 | 0.06 | 0.01 | 0.10 | 0.01 | 0.03 | 0.01 | 0.05 | 0.05 | 0.03 | 0.03 | 0.01 | 0.00 | 0.02 | 0.02 | 0.01 | 0.04 | 0.10 | 0.00 | 0.00 | 0.05 | 0.06 | 0.03 | 0.01 | 0.00 | 0.00 | 0.00 | 0.05 | 0.03 | 0.21 | 0.07 | 0.08 | 0.00 | 0.10 | 0.02 | 0.22 | 0.00 | 0.04 | 0.09 | 0.17 | 0.01 | 0.00 | 0.00 | 0.02 | 0.02 | 0.00 | 0.00 | 0.01 | 0.02 | 0.05 | 0.00 | 0.01 | 0.03 |
| MKNK2 | ENSG00000099875 | 0.00 | 0.01 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.05 | 0.04 | 0.13 | 0.05 | 0.00 | 0.03 | 0.10 | 0.02 | 0.09 | 0.03 | 0.13 | 0.02 | 0.14 | 0.02 | 0.17 | 0.02 | 0.09 | 0.01 | 0.05 | 0.01 | 0.09 | 0.00 | 0.07 | 0.04 | 0.13 | 0.00 | 0.03 | 0.19 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.02 | 0.17 | 0.04 | 0.90 | 0.08 | 0.19 | 0.01 | 0.27 | 0.04 | 0.77 | 0.17 | 0.16 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 | 0.07 | 0.04 | 0.02 | 0.07 | 0.01 | 0.02 | 0.02 | 0.03 | 0.07 |
| SLC44A2 | ENSG00000129353 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.02 | 0.11 | 0.04 | 0.00 | 0.01 | 0.09 | 0.01 | 0.01 | 0.05 | 0.07 | 0.06 | 0.06 | 0.04 | 0.09 | 0.06 | 0.08 | 0.03 | 0.03 | 0.01 | 0.03 | 0.03 | 0.01 | 0.03 | 0.02 | 0.11 | 0.00 | 0.01 | 0.14 | 0.03 | 0.00 | 0.00 | 0.00 | 0.01 | 0.10 | 0.04 | 0.58 | 0.18 | 0.11 | 0.05 | 0.28 | 0.06 | 0.83 | 0.10 | 0.28 | 0.02 | 0.02 | 0.00 | 0.03 | 0.00 | 0.00 | 0.03 | 0.02 | 0.00 | 0.05 | 0.01 | 0.02 | 0.02 | 0.02 | 0.02 |
| DHRS7 | ENSG00000100612 | 0.00 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.03 | 0.02 | 0.04 | 0.00 | 0.03 | 0.00 | 0.03 | 0.06 | 0.03 | 0.02 | 0.05 | 0.07 | 0.01 | 0.04 | 0.01 | 0.05 | 0.03 | 0.00 | 0.03 | 0.02 | 0.02 | 0.02 | 0.00 | 0.01 | 0.07 | 0.05 | 0.19 | 0.00 | 0.03 | 0.01 | 0.03 | 0.00 | 0.00 | 0.04 | 0.05 | 0.04 | 0.23 | 0.02 | 0.01 | 0.01 | 0.02 | 0.00 | 0.06 | 0.02 | 0.11 | 0.00 | 0.01 | 0.00 | 0.00 | 0.04 | 0.00 | 0.00 | 0.07 | 0.01 | 0.06 | 0.03 | 0.00 | 0.01 | 0.03 |
| EIF2AK2 | ENSG00000055332 | 0.00 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.06 | 0.06 | 0.01 | 0.00 | 0.00 | 0.01 | 0.05 | 0.07 | 0.02 | 0.08 | 0.02 | 0.03 | 0.01 | 0.03 | 0.03 | 0.03 | 0.03 | 0.00 | 0.01 | 0.00 | 0.03 | 0.01 | 0.03 | 0.05 | 0.00 | 0.00 | 0.05 | 0.00 | 0.04 | 0.00 | 0.01 | 0.00 | 0.00 | 0.05 | 0.02 | 0.20 | 0.05 | 0.07 | 0.00 | 0.07 | 0.02 | 0.16 | 0.00 | 0.07 | 0.06 | 0.13 | 0.01 | 0.00 | 0.00 | 0.10 | 0.06 | 0.01 | 0.01 | 0.01 | 0.01 | 0.03 | 0.00 | 0.01 | 0.01 |
| SLCO1B1 | ENSG00000134538 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.02 | 0.06 | 0.07 | 0.04 | 0.01 | 0.00 | 0.00 | 0.04 | 0.18 | 0.05 | 0.17 | 0.01 | 0.08 | 0.02 | 0.14 | 0.01 | 0.12 | 0.04 | 0.02 | 0.01 | 0.10 | 0.02 | 0.08 | 0.04 | 0.00 | 0.04 | 0.14 | 0.07 | 0.05 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.08 | 0.04 | 0.31 | 0.06 | 0.01 | 0.01 | 0.05 | 0.02 | 0.13 | 0.03 | 0.15 | 0.10 | 0.63 | 0.00 | 0.00 | 0.01 | 0.00 | 0.04 | 0.06 | 0.01 | 0.03 | 0.04 | 0.00 | 0.00 | 0.06 | 0.01 |
| BAZ1B | ENSG00000009954 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.05 | 0.02 | 0.00 | 0.00 | 0.02 | 0.00 | 0.02 | 0.02 | 0.10 | 0.02 | 0.04 | 0.03 | 0.17 | 0.03 | 0.09 | 0.02 | 0.01 | 0.00 | 0.01 | 0.00 | 0.02 | 0.00 | 0.08 | 0.01 | 0.00 | 0.01 | 0.15 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.09 | 0.02 | 0.17 | 0.06 | 0.04 | 0.01 | 0.06 | 0.02 | 0.12 | 0.00 | 0.07 | 0.03 | 0.12 | 0.00 | 0.00 | 0.00 | 0.10 | 0.00 | 0.01 | 0.01 | 0.05 | 0.00 | 0.00 | 0.00 | 0.06 | 0.02 |
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