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 |
| EEF2K | ENSG00000103319 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.13 | 0.04 | 0.00 | 0.00 | 0.00 | 0.04 | 0.03 | 0.02 | 0.04 | 0.02 | 0.02 | 0.02 | 0.03 | 0.02 | 0.02 | 0.01 | 0.02 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 | 0.10 | 0.06 | 0.01 | 0.01 | 0.03 | 0.01 | 0.15 | 0.00 | 0.02 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.09 | 0.00 | 0.00 | 0.02 | 0.00 | 0.07 | 0.00 | 0.00 | 0.01 | 0.03 |
| AQP8 | ENSG00000103375 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.16 | 0.03 | 0.00 | 0.00 | 0.00 | 0.06 | 0.04 | 0.01 | 0.12 | 0.01 | 0.03 | 0.02 | 0.07 | 0.00 | 0.05 | 0.00 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.04 | 0.01 | 0.00 | 0.02 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.04 | 0.00 | 0.07 | 0.05 | 0.02 | 0.01 | 0.05 | 0.01 | 0.17 | 0.03 | 0.02 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.06 | 0.00 | 0.00 | 0.02 | 0.00 | 0.05 | 0.00 | 0.00 | 0.01 | 0.02 |
| XYLT1 | ENSG00000103489 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.11 | 0.06 | 0.00 | 0.00 | 0.01 | 0.02 | 0.02 | 0.02 | 0.04 | 0.03 | 0.02 | 0.02 | 0.07 | 0.03 | 0.05 | 0.02 | 0.02 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.05 | 0.01 | 0.00 | 0.05 | 0.02 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.05 | 0.02 | 0.15 | 0.07 | 0.07 | 0.00 | 0.07 | 0.01 | 0.20 | 0.00 | 0.04 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.11 | 0.00 | 0.01 | 0.01 | 0.00 | 0.02 | 0.03 | 0.00 | 0.03 | 0.01 |
| PYCARD | ENSG00000103490 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.09 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.10 | 0.01 | 0.10 | 0.01 | 0.02 | 0.02 | 0.07 | 0.00 | 0.06 | 0.00 | 0.05 | 0.00 | 0.06 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.08 | 0.01 | 0.09 | 0.03 | 0.02 | 0.03 | 0.11 | 0.00 | 0.52 | 0.05 | 0.06 | 0.02 | 0.02 | 0.01 | 0.00 | 0.02 | 0.05 | 0.00 | 0.01 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.01 |
| BCKDK | ENSG00000103507 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.09 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.10 | 0.01 | 0.10 | 0.01 | 0.03 | 0.02 | 0.07 | 0.00 | 0.06 | 0.00 | 0.05 | 0.00 | 0.06 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.09 | 0.01 | 0.08 | 0.03 | 0.02 | 0.03 | 0.11 | 0.00 | 0.52 | 0.05 | 0.06 | 0.02 | 0.02 | 0.01 | 0.00 | 0.02 | 0.05 | 0.00 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.01 |
| KAT8 | ENSG00000103510 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.09 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.10 | 0.01 | 0.10 | 0.01 | 0.03 | 0.02 | 0.07 | 0.00 | 0.06 | 0.00 | 0.05 | 0.00 | 0.06 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.09 | 0.01 | 0.08 | 0.03 | 0.02 | 0.03 | 0.12 | 0.00 | 0.52 | 0.05 | 0.06 | 0.02 | 0.02 | 0.01 | 0.00 | 0.02 | 0.05 | 0.00 | 0.01 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.01 |
| LACTB | ENSG00000103642 | 0.00 | 0.00 | 0.00 | 0.01 | 0.14 | 0.00 | 0.01 | 0.02 | 0.02 | 0.03 | 0.00 | 0.00 | 0.08 | 0.00 | 0.03 | 0.03 | 0.05 | 0.03 | 0.02 | 0.02 | 0.03 | 0.03 | 0.05 | 0.03 | 0.01 | 0.02 | 0.00 | 0.02 | 0.02 | 0.01 | 0.03 | 0.01 | 0.00 | 0.01 | 0.04 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.05 | 0.09 | 0.11 | 0.05 | 0.01 | 0.03 | 0.05 | 0.07 | 0.19 | 0.11 | 0.01 | 0.01 | 0.02 | 0.00 | 0.00 | 0.06 | 0.00 | 0.01 | 0.01 | 0.01 | 0.03 | 0.00 | 0.00 | 0.03 | 0.02 |
| CA2 | ENSG00000104267 | 0.01 | 0.00 | 0.00 | 0.01 | 0.06 | 0.00 | 0.07 | 0.01 | 0.16 | 0.01 | 0.00 | 0.00 | 0.02 | 0.00 | 0.14 | 0.01 | 0.14 | 0.02 | 0.06 | 0.01 | 0.16 | 0.00 | 0.12 | 0.00 | 0.09 | 0.00 | 0.13 | 0.03 | 0.02 | 0.02 | 0.15 | 0.00 | 0.20 | 0.01 | 0.06 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.27 | 0.01 | 0.27 | 0.11 | 0.05 | 0.01 | 0.06 | 0.01 | 0.21 | 0.04 | 0.20 | 0.05 | 0.17 | 0.00 | 0.00 | 0.00 | 0.04 | 0.02 | 0.02 | 0.00 | 0.01 | 0.01 | 0.22 | 0.00 | 0.11 | 0.01 |
| FZD3 | ENSG00000104290 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.13 | 0.01 | 0.10 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 | 0.06 | 0.02 | 0.08 | 0.01 | 0.03 | 0.08 | 0.07 | 0.05 | 0.04 | 0.04 | 0.08 | 0.03 | 0.16 | 0.02 | 0.03 | 0.02 | 0.10 | 0.00 | 0.08 | 0.07 | 0.00 | 0.02 | 0.02 | 0.00 | 0.00 | 0.02 | 0.13 | 0.04 | 0.34 | 0.00 | 0.02 | 0.03 | 0.08 | 0.05 | 0.14 | 0.04 | 0.08 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.01 | 0.02 | 0.05 |
| TRPA1 | ENSG00000104321 | 0.01 | 0.00 | 0.00 | 0.01 | 0.06 | 0.00 | 0.06 | 0.01 | 0.10 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.14 | 0.02 | 0.08 | 0.02 | 0.07 | 0.01 | 0.08 | 0.01 | 0.11 | 0.01 | 0.05 | 0.00 | 0.15 | 0.03 | 0.01 | 0.01 | 0.07 | 0.00 | 0.05 | 0.02 | 0.04 | 0.00 | 0.01 | 0.02 | 0.00 | 0.00 | 0.20 | 0.01 | 0.32 | 0.07 | 0.04 | 0.02 | 0.12 | 0.01 | 0.52 | 0.02 | 0.18 | 0.06 | 0.21 | 0.00 | 0.01 | 0.00 | 0.00 | 0.05 | 0.01 | 0.01 | 0.00 | 0.02 | 0.22 | 0.00 | 0.06 | 0.01 |
| DKK4 | ENSG00000104371 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.10 | 0.21 | 0.05 | 0.00 | 0.00 | 0.04 | 0.00 | 0.20 | 0.04 | 0.40 | 0.03 | 0.11 | 0.03 | 0.45 | 0.07 | 0.08 | 0.04 | 0.18 | 0.02 | 0.16 | 0.04 | 0.02 | 0.00 | 0.03 | 0.04 | 0.00 | 0.02 | 0.09 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.41 | 0.05 | 0.34 | 0.04 | 0.08 | 0.03 | 0.18 | 0.01 | 0.80 | 0.07 | 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 |
| WISP1 | ENSG00000104415 | 0.02 | 0.00 | 0.02 | 0.00 | 0.09 | 0.00 | 0.08 | 0.02 | 0.21 | 0.03 | 0.02 | 0.00 | 0.10 | 0.02 | 0.28 | 0.01 | 0.34 | 0.00 | 0.29 | 0.00 | 0.52 | 0.01 | 0.21 | 0.01 | 0.18 | 0.01 | 0.23 | 0.01 | 0.15 | 0.00 | 0.37 | 0.01 | 0.25 | 0.01 | 0.10 | 0.00 | 0.01 | 0.02 | 0.00 | 0.01 | 0.47 | 0.03 | 1.62 | 0.03 | 0.20 | 0.00 | 0.18 | 0.01 | 0.37 | 0.03 | 0.15 | 0.06 | 0.03 | 0.02 | 0.02 | 0.00 | 0.17 | 0.00 | 0.18 | 0.01 | 0.03 | 0.02 | 0.50 | 0.00 | 0.22 | 0.01 |
| IL7 | ENSG00000104432 | 0.01 | 0.00 | 0.01 | 0.00 | 0.10 | 0.00 | 0.07 | 0.01 | 0.12 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.18 | 0.02 | 0.13 | 0.03 | 0.05 | 0.01 | 0.13 | 0.01 | 0.11 | 0.01 | 0.09 | 0.00 | 0.15 | 0.01 | 0.02 | 0.01 | 0.10 | 0.00 | 0.19 | 0.01 | 0.08 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.23 | 0.01 | 0.27 | 0.09 | 0.04 | 0.00 | 0.05 | 0.01 | 0.15 | 0.02 | 0.14 | 0.07 | 0.17 | 0.00 | 0.00 | 0.00 | 0.04 | 0.00 | 0.01 | 0.01 | 0.00 | 0.01 | 0.22 | 0.00 | 0.11 | 0.01 |
| TULP2 | ENSG00000104804 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.04 | 0.07 | 0.04 | 0.00 | 0.02 | 0.00 | 0.06 | 0.01 | 0.08 | 0.04 | 0.10 | 0.02 | 0.02 | 0.06 | 0.05 | 0.06 | 0.03 | 0.01 | 0.03 | 0.01 | 0.03 | 0.03 | 0.05 | 0.05 | 0.03 | 0.00 | 0.07 | 0.19 | 0.02 | 0.00 | 0.03 | 0.00 | 0.00 | 0.08 | 0.05 | 0.05 | 0.33 | 0.05 | 0.07 | 0.03 | 0.06 | 0.21 | 0.19 | 0.04 | 0.18 | 0.00 | 0.04 | 0.01 | 0.00 | 0.07 | 0.05 | 0.00 | 0.14 | 0.01 | 0.13 | 0.00 | 0.00 | 0.02 | 0.02 |
| CGB2 | ENSG00000104818 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.03 | 0.08 | 0.04 | 0.00 | 0.02 | 0.00 | 0.06 | 0.01 | 0.07 | 0.04 | 0.10 | 0.03 | 0.02 | 0.08 | 0.05 | 0.06 | 0.03 | 0.01 | 0.03 | 0.01 | 0.03 | 0.03 | 0.05 | 0.04 | 0.03 | 0.00 | 0.07 | 0.17 | 0.02 | 0.00 | 0.03 | 0.00 | 0.00 | 0.08 | 0.05 | 0.05 | 0.31 | 0.05 | 0.07 | 0.03 | 0.05 | 0.17 | 0.19 | 0.04 | 0.18 | 0.00 | 0.04 | 0.01 | 0.00 | 0.07 | 0.05 | 0.00 | 0.14 | 0.01 | 0.13 | 0.00 | 0.00 | 0.02 | 0.02 |
| LHB | ENSG00000104826 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.03 | 0.08 | 0.04 | 0.00 | 0.02 | 0.00 | 0.06 | 0.01 | 0.07 | 0.04 | 0.10 | 0.03 | 0.02 | 0.08 | 0.05 | 0.06 | 0.03 | 0.01 | 0.03 | 0.01 | 0.03 | 0.03 | 0.05 | 0.04 | 0.03 | 0.00 | 0.07 | 0.17 | 0.02 | 0.00 | 0.03 | 0.00 | 0.00 | 0.08 | 0.05 | 0.05 | 0.32 | 0.05 | 0.07 | 0.03 | 0.05 | 0.17 | 0.19 | 0.02 | 0.18 | 0.00 | 0.04 | 0.01 | 0.01 | 0.07 | 0.05 | 0.00 | 0.14 | 0.01 | 0.13 | 0.00 | 0.00 | 0.02 | 0.02 |
| CGB | ENSG00000104827 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.03 | 0.08 | 0.04 | 0.00 | 0.02 | 0.00 | 0.06 | 0.01 | 0.07 | 0.04 | 0.10 | 0.03 | 0.02 | 0.08 | 0.05 | 0.06 | 0.03 | 0.01 | 0.03 | 0.01 | 0.03 | 0.03 | 0.05 | 0.04 | 0.03 | 0.00 | 0.07 | 0.17 | 0.02 | 0.00 | 0.03 | 0.00 | 0.00 | 0.08 | 0.05 | 0.05 | 0.32 | 0.05 | 0.07 | 0.03 | 0.05 | 0.17 | 0.19 | 0.02 | 0.18 | 0.00 | 0.04 | 0.01 | 0.01 | 0.07 | 0.05 | 0.00 | 0.14 | 0.01 | 0.13 | 0.00 | 0.00 | 0.02 | 0.02 |
| TUBB4A | ENSG00000104833 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.02 | 0.01 | 0.03 | 0.03 | 0.09 | 0.00 | 0.01 | 0.01 | 0.09 | 0.01 | 0.06 | 0.03 | 0.09 | 0.01 | 0.09 | 0.02 | 0.11 | 0.01 | 0.08 | 0.03 | 0.02 | 0.01 | 0.06 | 0.00 | 0.05 | 0.01 | 0.12 | 0.00 | 0.01 | 0.01 | 0.04 | 0.01 | 0.00 | 0.00 | 0.00 | 0.04 | 0.08 | 0.11 | 0.56 | 0.03 | 0.17 | 0.01 | 0.21 | 0.02 | 0.56 | 0.17 | 0.02 | 0.02 | 0.00 | 0.00 | 0.01 | 0.00 | 0.11 | 0.01 | 0.01 | 0.02 | 0.01 | 0.00 | 0.05 | 0.04 | 0.03 |
| KCNA7 | ENSG00000104848 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.03 | 0.09 | 0.04 | 0.00 | 0.02 | 0.00 | 0.06 | 0.01 | 0.07 | 0.04 | 0.10 | 0.03 | 0.02 | 0.08 | 0.05 | 0.07 | 0.03 | 0.01 | 0.03 | 0.01 | 0.03 | 0.03 | 0.05 | 0.04 | 0.03 | 0.00 | 0.07 | 0.17 | 0.02 | 0.00 | 0.03 | 0.00 | 0.00 | 0.08 | 0.05 | 0.05 | 0.32 | 0.05 | 0.07 | 0.03 | 0.05 | 0.15 | 0.19 | 0.04 | 0.18 | 0.00 | 0.04 | 0.01 | 0.00 | 0.07 | 0.05 | 0.00 | 0.14 | 0.01 | 0.13 | 0.00 | 0.00 | 0.02 | 0.02 |
| SLC17A7 | ENSG00000104888 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.01 | 0.11 | 0.04 | 0.00 | 0.02 | 0.00 | 0.06 | 0.02 | 0.07 | 0.05 | 0.10 | 0.03 | 0.02 | 0.07 | 0.05 | 0.07 | 0.03 | 0.01 | 0.02 | 0.02 | 0.03 | 0.03 | 0.05 | 0.05 | 0.04 | 0.00 | 0.07 | 0.26 | 0.02 | 0.00 | 0.03 | 0.00 | 0.00 | 0.11 | 0.04 | 0.05 | 0.31 | 0.05 | 0.06 | 0.06 | 0.05 | 0.10 | 0.18 | 0.04 | 0.18 | 0.00 | 0.04 | 0.01 | 0.00 | 0.07 | 0.05 | 0.01 | 0.13 | 0.03 | 0.12 | 0.00 | 0.00 | 0.02 | 0.02 |
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