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 |
| EHMT1 | ENSG00000181090 | 0.01 | 0.01 | 0.01 | 0.01 | 0.00 | 0.08 | 0.04 | 0.01 | 0.05 | 0.03 | 0.00 | 0.00 | 0.00 | 0.02 | 0.08 | 0.04 | 0.07 | 0.03 | 0.11 | 0.05 | 0.19 | 0.01 | 0.14 | 0.02 | 0.03 | 0.01 | 0.10 | 0.04 | 0.02 | 0.00 | 0.05 | 0.05 | 0.07 | 0.01 | 0.12 | 0.03 | 0.00 | 0.02 | 0.00 | 0.00 | 0.06 | 0.07 | 0.22 | 0.22 | 0.08 | 0.03 | 0.04 | 0.04 | 0.07 | 0.14 | 0.11 | 0.19 | 0.03 | 0.06 | 0.03 | 0.00 | 0.05 | 0.00 | 0.04 | 0.01 | 0.05 | 0.02 | 0.00 | 0.00 | 0.04 | 0.03 |
| PHF14 | ENSG00000106443 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.02 | 0.02 | 0.14 | 0.02 | 0.01 | 0.01 | 0.08 | 0.01 | 0.09 | 0.01 | 0.12 | 0.02 | 0.08 | 0.01 | 0.16 | 0.03 | 0.10 | 0.01 | 0.04 | 0.01 | 0.04 | 0.00 | 0.01 | 0.00 | 0.06 | 0.01 | 0.01 | 0.01 | 0.11 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.06 | 0.04 | 0.10 | 0.36 | 0.02 | 0.02 | 0.06 | 0.05 | 0.08 | 0.03 | 0.17 | 0.06 | 0.10 | 0.00 | 0.00 | 0.01 | 0.03 | 0.03 | 0.00 | 0.02 | 0.04 | 0.01 | 0.00 | 0.00 | 0.12 | 0.00 |
| NPC1 | ENSG00000141458 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 | 0.10 | 0.02 | 0.00 | 0.00 | 0.03 | 0.01 | 0.13 | 0.01 | 0.22 | 0.02 | 0.16 | 0.03 | 0.45 | 0.01 | 0.26 | 0.03 | 0.01 | 0.02 | 0.07 | 0.02 | 0.27 | 0.02 | 0.00 | 0.01 | 0.04 | 0.03 | 0.09 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.02 | 0.31 | 0.04 | 0.02 | 0.03 | 0.11 | 0.01 | 0.00 | 0.07 | 0.09 | 0.03 | 0.00 | 0.03 | 0.00 | 0.01 | 0.03 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 |
| SLC20A2 | ENSG00000168575 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.09 | 0.21 | 0.05 | 0.00 | 0.00 | 0.04 | 0.00 | 0.20 | 0.04 | 0.42 | 0.04 | 0.12 | 0.03 | 0.45 | 0.07 | 0.09 | 0.04 | 0.18 | 0.03 | 0.16 | 0.05 | 0.02 | 0.00 | 0.04 | 0.04 | 0.01 | 0.02 | 0.09 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.41 | 0.05 | 0.35 | 0.04 | 0.08 | 0.03 | 0.19 | 0.01 | 0.87 | 0.10 | 0.14 | 0.07 | 0.02 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.01 | 0.05 | 0.02 |
| SLC41A2 | ENSG00000136052 | 0.01 | 0.01 | 0.02 | 0.00 | 0.06 | 0.02 | 0.04 | 0.03 | 0.06 | 0.03 | 0.00 | 0.00 | 0.04 | 0.02 | 0.02 | 0.05 | 0.02 | 0.05 | 0.01 | 0.03 | 0.04 | 0.05 | 0.03 | 0.04 | 0.00 | 0.01 | 0.02 | 0.03 | 0.00 | 0.06 | 0.03 | 0.04 | 0.00 | 0.22 | 0.01 | 0.02 | 0.00 | 0.03 | 0.00 | 0.00 | 0.03 | 0.08 | 0.07 | 0.22 | 0.01 | 0.01 | 0.02 | 0.04 | 0.02 | 0.11 | 0.15 | 0.04 | 0.00 | 0.01 | 0.00 | 0.00 | 0.10 | 0.00 | 0.01 | 0.02 | 0.01 | 0.01 | 0.00 | 0.00 | 0.02 | 0.08 |
| GAA | ENSG00000171298 | 0.02 | 0.00 | 0.06 | 0.00 | 0.02 | 0.00 | 0.04 | 0.03 | 0.20 | 0.00 | 0.00 | 0.00 | 0.09 | 0.02 | 0.18 | 0.01 | 0.20 | 0.04 | 0.07 | 0.05 | 0.18 | 0.08 | 0.09 | 0.03 | 0.05 | 0.01 | 0.04 | 0.03 | 0.02 | 0.09 | 0.29 | 0.01 | 0.10 | 0.01 | 0.25 | 0.00 | 0.02 | 0.01 | 0.00 | 0.00 | 0.35 | 0.03 | 0.43 | 0.04 | 0.11 | 0.09 | 0.16 | 0.01 | 0.54 | 0.07 | 0.18 | 0.05 | 0.06 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.06 | 0.00 | 0.04 | 0.02 | 0.17 | 0.00 | 0.24 | 0.01 |
| MECR | ENSG00000116353 | 0.00 | 0.05 | 0.00 | 0.06 | 0.00 | 0.00 | 0.00 | 0.02 | 0.06 | 0.07 | 0.00 | 0.01 | 0.05 | 0.17 | 0.05 | 0.05 | 0.03 | 0.08 | 0.03 | 0.05 | 0.05 | 0.11 | 0.02 | 0.11 | 0.00 | 0.15 | 0.00 | 0.21 | 0.00 | 0.09 | 0.00 | 0.21 | 0.00 | 0.92 | 0.00 | 0.07 | 0.02 | 0.08 | 0.00 | 0.00 | 0.02 | 0.14 | 0.12 | 0.37 | 0.04 | 0.05 | 0.03 | 0.11 | 0.00 | 0.08 | 0.12 | 0.09 | 0.04 | 0.04 | 0.02 | 0.00 | 0.00 | 0.07 | 0.00 | 0.01 | 0.03 | 0.05 | 0.00 | 0.07 | 0.06 | 0.05 |
| DLD | ENSG00000091140 | 0.01 | 0.00 | 0.05 | 0.01 | 0.01 | 0.00 | 0.04 | 0.03 | 0.05 | 0.02 | 0.00 | 0.00 | 0.03 | 0.02 | 0.09 | 0.02 | 0.14 | 0.03 | 0.16 | 0.02 | 0.33 | 0.07 | 0.09 | 0.04 | 0.01 | 0.01 | 0.01 | 0.00 | 0.03 | 0.02 | 0.06 | 0.02 | 0.00 | 0.02 | 0.02 | 0.06 | 0.00 | 0.02 | 0.00 | 0.00 | 0.06 | 0.04 | 0.26 | 0.06 | 0.04 | 0.04 | 0.04 | 0.03 | 0.16 | 0.09 | 0.17 | 0.02 | 0.08 | 0.01 | 0.00 | 0.02 | 0.13 | 0.00 | 0.09 | 0.00 | 0.02 | 0.01 | 0.00 | 0.00 | 0.08 | 0.03 |
| IGSF8 | ENSG00000162729 | 0.03 | 0.00 | 0.01 | 0.01 | 0.00 | 0.03 | 0.02 | 0.04 | 0.76 | 0.00 | 0.02 | 0.00 | 0.10 | 0.01 | 0.28 | 0.00 | 0.28 | 0.00 | 0.06 | 0.00 | 0.27 | 0.00 | 0.12 | 0.00 | 0.03 | 0.00 | 0.11 | 0.00 | 0.06 | 0.00 | 0.28 | 0.00 | 0.30 | 0.01 | 0.16 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.28 | 0.01 | 0.42 | 0.02 | 0.16 | 0.00 | 0.15 | 0.00 | 0.28 | 0.00 | 0.49 | 0.02 | 0.10 | 0.00 | 0.00 | 0.00 | 0.24 | 0.00 | 0.02 | 0.00 | 0.05 | 0.00 | 0.00 | 0.00 | 0.16 | 0.00 |
| RTN4 | ENSG00000115310 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.04 | 0.10 | 0.00 | 0.00 | 0.00 | 0.01 | 0.03 | 0.06 | 0.01 | 0.26 | 0.01 | 0.04 | 0.01 | 0.06 | 0.03 | 0.02 | 0.01 | 0.00 | 0.01 | 0.02 | 0.01 | 0.01 | 0.01 | 0.04 | 0.02 | 0.00 | 0.02 | 0.04 | 0.03 | 0.00 | 0.01 | 0.00 | 0.00 | 0.07 | 0.01 | 0.23 | 0.05 | 0.03 | 0.01 | 0.05 | 0.02 | 0.21 | 0.09 | 0.07 | 0.05 | 0.07 | 0.02 | 0.00 | 0.00 | 0.17 | 0.00 | 0.01 | 0.01 | 0.01 | 0.00 | 0.03 | 0.00 | 0.01 | 0.01 |
| SETD4 | ENSG00000185917 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 | 0.08 | 0.03 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 | 0.03 | 0.02 | 0.05 | 0.03 | 0.03 | 0.03 | 0.04 | 0.05 | 0.05 | 0.02 | 0.02 | 0.05 | 0.05 | 0.01 | 0.01 | 0.01 | 0.01 | 0.05 | 0.03 | 0.08 | 0.04 | 0.01 | 0.00 | 0.00 | 0.00 | 0.07 | 0.02 | 0.12 | 0.08 | 0.10 | 0.01 | 0.02 | 0.01 | 0.00 | 0.03 | 0.05 | 0.07 | 0.03 | 0.00 | 0.07 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.02 | 0.03 | 0.00 | 0.01 | 0.01 |
| SLC30A9 | ENSG00000014824 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.01 | 0.06 | 0.02 | 0.04 | 0.00 | 0.00 | 0.00 | 0.06 | 0.08 | 0.02 | 0.06 | 0.03 | 0.04 | 0.02 | 0.07 | 0.03 | 0.02 | 0.03 | 0.01 | 0.01 | 0.02 | 0.05 | 0.01 | 0.01 | 0.04 | 0.01 | 0.00 | 0.07 | 0.03 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.03 | 0.03 | 0.10 | 0.08 | 0.00 | 0.02 | 0.01 | 0.03 | 0.13 | 0.07 | 0.05 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.05 | 0.00 | 0.07 | 0.01 |
| STIM2 | ENSG00000109689 | 0.01 | 0.00 | 0.00 | 0.00 | 0.04 | 0.00 | 0.00 | 0.05 | 0.02 | 0.04 | 0.00 | 0.00 | 0.00 | 0.01 | 0.07 | 0.02 | 0.04 | 0.06 | 0.06 | 0.04 | 0.05 | 0.04 | 0.01 | 0.01 | 0.02 | 0.02 | 0.03 | 0.01 | 0.00 | 0.01 | 0.02 | 0.03 | 0.00 | 0.01 | 0.05 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.04 | 0.09 | 0.08 | 0.01 | 0.04 | 0.02 | 0.04 | 0.06 | 0.07 | 0.08 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.02 | 0.05 | 0.00 | 0.04 | 0.01 |
| CLK1 | ENSG00000013441 | 0.03 | 0.03 | 0.04 | 0.01 | 0.00 | 0.01 | 0.02 | 0.01 | 0.01 | 0.11 | 0.00 | 0.00 | 0.00 | 0.04 | 0.05 | 0.02 | 0.18 | 0.06 | 0.10 | 0.09 | 0.11 | 0.04 | 0.07 | 0.03 | 0.02 | 0.01 | 0.04 | 0.00 | 0.07 | 0.00 | 0.08 | 0.01 | 0.05 | 0.01 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.06 | 0.03 | 0.27 | 0.08 | 0.14 | 0.11 | 0.05 | 0.02 | 0.06 | 0.05 | 0.06 | 0.09 | 0.06 | 0.00 | 0.00 | 0.01 | 0.00 | 0.04 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.02 | 0.02 | 0.03 |
| RGS12 | ENSG00000159788 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.03 | 0.03 | 0.08 | 0.04 | 0.00 | 0.02 | 0.00 | 0.03 | 0.04 | 0.04 | 0.04 | 0.05 | 0.03 | 0.06 | 0.04 | 0.08 | 0.06 | 0.06 | 0.02 | 0.03 | 0.04 | 0.03 | 0.01 | 0.02 | 0.04 | 0.07 | 0.00 | 0.01 | 0.08 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.03 | 0.06 | 0.29 | 0.07 | 0.02 | 0.05 | 0.07 | 0.05 | 0.21 | 0.00 | 0.12 | 0.04 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.02 | 0.00 | 0.01 | 0.01 | 0.02 | 0.00 | 0.04 | 0.05 |
| PDE4A | ENSG00000065989 | 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 | 0.02 | 0.05 | 0.09 | 0.06 | 0.05 | 0.04 | 0.07 | 0.06 | 0.06 | 0.04 | 0.03 | 0.01 | 0.02 | 0.04 | 0.01 | 0.03 | 0.04 | 0.12 | 0.00 | 0.01 | 0.13 | 0.03 | 0.00 | 0.00 | 0.00 | 0.01 | 0.10 | 0.04 | 0.58 | 0.19 | 0.13 | 0.05 | 0.25 | 0.08 | 0.81 | 0.18 | 0.27 | 0.02 | 0.02 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.05 | 0.01 | 0.02 | 0.02 | 0.02 | 0.02 |
| IDS | ENSG00000010404 | 0.03 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.04 | 0.03 | 0.10 | 0.04 | 0.06 | 0.00 | 0.06 | 0.05 | 0.17 | 0.01 | 0.15 | 0.02 | 0.11 | 0.00 | 0.15 | 0.02 | 0.15 | 0.03 | 0.04 | 0.01 | 0.08 | 0.02 | 0.06 | 0.01 | 0.11 | 0.02 | 0.00 | 0.01 | 0.07 | 0.03 | 0.01 | 0.00 | 0.00 | 0.00 | 0.09 | 0.02 | 0.41 | 0.10 | 0.19 | 0.02 | 0.06 | 0.02 | 0.04 | 0.10 | 0.16 | 0.12 | 0.00 | 0.02 | 0.00 | 0.00 | 0.10 | 0.04 | 0.02 | 0.03 | 0.02 | 0.02 | 0.05 | 0.00 | 0.07 | 0.02 |
| SCYL3 | ENSG00000000457 | 0.03 | 0.00 | 0.01 | 0.01 | 0.00 | 0.03 | 0.00 | 0.05 | 0.43 | 0.01 | 0.02 | 0.02 | 0.10 | 0.03 | 0.13 | 0.01 | 0.25 | 0.01 | 0.04 | 0.00 | 0.20 | 0.01 | 0.11 | 0.01 | 0.03 | 0.00 | 0.11 | 0.00 | 0.06 | 0.00 | 0.23 | 0.00 | 0.22 | 0.05 | 0.00 | 0.06 | 0.04 | 0.00 | 0.00 | 0.00 | 0.19 | 0.02 | 0.32 | 0.02 | 0.11 | 0.01 | 0.10 | 0.00 | 0.29 | 0.00 | 0.58 | 0.03 | 0.10 | 0.00 | 0.00 | 0.00 | 0.36 | 0.04 | 0.01 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.15 | 0.01 |
| F13A1 | ENSG00000124491 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.07 | 0.26 | 0.06 | 0.00 | 0.05 | 0.02 | 0.01 | 0.11 | 0.02 | 0.09 | 0.08 | 0.05 | 0.06 | 0.07 | 0.22 | 0.05 | 0.11 | 0.02 | 0.03 | 0.02 | 0.04 | 0.00 | 0.08 | 0.15 | 0.02 | 0.06 | 0.06 | 0.03 | 0.03 | 0.00 | 0.01 | 0.00 | 0.00 | 0.11 | 0.07 | 0.47 | 0.10 | 0.11 | 0.06 | 0.09 | 0.02 | 0.23 | 0.05 | 0.06 | 0.14 | 0.04 | 0.03 | 0.00 | 0.00 | 0.10 | 0.01 | 0.02 | 0.03 | 0.02 | 0.03 | 0.19 | 0.00 | 0.24 | 0.00 |
| PMS2 | ENSG00000122512 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 | 0.16 | 0.02 | 0.00 | 0.00 | 0.08 | 0.00 | 0.11 | 0.02 | 0.13 | 0.01 | 0.10 | 0.01 | 0.20 | 0.02 | 0.14 | 0.01 | 0.05 | 0.00 | 0.04 | 0.00 | 0.02 | 0.00 | 0.06 | 0.01 | 0.01 | 0.01 | 0.12 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.06 | 0.05 | 0.09 | 0.41 | 0.02 | 0.02 | 0.03 | 0.06 | 0.09 | 0.03 | 0.24 | 0.04 | 0.18 | 0.01 | 0.00 | 0.01 | 0.10 | 0.00 | 0.01 | 0.02 | 0.04 | 0.01 | 0.00 | 0.00 | 0.17 | 0.01 |
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