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 |
| ARAF | ENSG00000078061 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.06 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.07 | 0.02 | 0.05 | 0.02 | 0.04 | 0.02 | 0.04 | 0.03 | 0.04 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.16 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.07 | 0.01 | 0.36 | 0.06 | 0.03 | 0.03 | 0.13 | 0.01 | 0.29 | 0.03 | 0.12 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.07 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.01 | 0.00 |
| EDN1 | ENSG00000078401 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.02 | 0.37 | 0.05 | 0.00 | 0.02 | 0.01 | 0.04 | 0.09 | 0.01 | 0.10 | 0.07 | 0.05 | 0.06 | 0.15 | 0.18 | 0.04 | 0.09 | 0.02 | 0.03 | 0.01 | 0.03 | 0.00 | 0.07 | 0.15 | 0.01 | 0.06 | 0.03 | 0.01 | 0.03 | 0.00 | 0.01 | 0.00 | 0.00 | 0.16 | 0.03 | 0.49 | 0.06 | 0.09 | 0.05 | 0.05 | 0.01 | 0.20 | 0.06 | 0.06 | 0.13 | 0.04 | 0.03 | 0.00 | 0.00 | 0.07 | 0.04 | 0.01 | 0.03 | 0.01 | 0.02 | 0.28 | 0.00 | 0.22 | 0.00 |
| FGF20 | ENSG00000078579 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.14 | 0.00 | 0.14 | 0.03 | 0.00 | 0.02 | 0.05 | 0.02 | 0.06 | 0.01 | 0.09 | 0.01 | 0.07 | 0.06 | 0.05 | 0.08 | 0.04 | 0.00 | 0.11 | 0.00 | 0.19 | 0.01 | 0.05 | 0.01 | 0.11 | 0.00 | 0.05 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.00 | 0.02 | 0.13 | 0.04 | 0.40 | 0.01 | 0.04 | 0.00 | 0.09 | 0.07 | 0.18 | 0.06 | 0.04 | 0.03 | 0.01 | 0.00 | 0.00 | 0.00 | 0.09 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.01 | 0.01 | 0.04 |
| P2RY10 | ENSG00000078589 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.02 | 0.05 | 0.02 | 0.04 | 0.01 | 0.07 | 0.02 | 0.02 | 0.01 | 0.01 | 0.01 | 0.01 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.02 | 0.10 | 0.03 | 0.03 | 0.02 | 0.03 | 0.01 | 0.01 | 0.05 | 0.17 | 0.10 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 | 0.03 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.02 | 0.01 |
| PKD2L2 | ENSG00000078795 | 0.28 | 0.00 | 0.03 | 0.01 | 0.00 | 0.00 | 0.03 | 0.03 | 0.03 | 0.03 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 | 0.04 | 0.01 | 0.03 | 0.01 | 0.03 | 0.03 | 0.03 | 0.02 | 0.06 | 0.01 | 0.02 | 0.02 | 0.02 | 0.01 | 0.01 | 0.08 | 0.02 | 0.09 | 0.01 | 0.24 | 0.02 | 0.00 | 0.06 | 0.01 | 0.00 | 0.03 | 0.02 | 0.12 | 0.12 | 0.03 | 0.02 | 0.03 | 0.01 | 0.10 | 0.01 | 0.07 | 0.04 | 0.00 | 0.00 | 0.00 | 0.10 | 0.04 | 0.00 | 0.01 | 0.04 | 0.01 | 0.02 | 0.00 | 0.03 | 0.03 | 0.12 |
| BPIFB2 | ENSG00000078898 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.02 | 0.01 | 0.23 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.07 | 0.01 | 0.21 | 0.00 | 0.20 | 0.00 | 0.06 | 0.00 | 0.05 | 0.01 | 0.11 | 0.00 | 0.18 | 0.00 | 0.03 | 0.01 | 0.02 | 0.00 | 0.00 | 0.01 | 0.05 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.06 | 0.02 | 0.22 | 0.02 | 0.22 | 0.00 | 0.07 | 0.01 | 0.29 | 0.00 | 0.08 | 0.02 | 0.03 | 0.00 | 0.00 | 0.02 | 0.04 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.06 | 0.00 |
| LXN | ENSG00000079257 | 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 | 0.11 | 0.01 | 1.02 | 0.00 | 0.47 | 0.00 | 0.66 | 0.01 | 0.16 | 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 | 0.73 | 0.02 | 0.49 | 0.01 | 0.17 | 0.01 | 0.21 | 0.02 | 0.07 | 0.06 | 0.12 | 0.00 | 0.00 | 0.00 | 0.04 | 0.00 | 0.01 | 0.01 | 0.02 | 0.03 | 0.00 | 0.00 | 0.01 | 0.03 |
| LIPE | ENSG00000079435 | 0.01 | 0.00 | 0.00 | 0.03 | 0.00 | 0.02 | 0.00 | 0.08 | 0.13 | 0.03 | 0.00 | 0.00 | 0.14 | 0.05 | 0.10 | 0.05 | 0.13 | 0.07 | 0.01 | 0.02 | 0.03 | 0.07 | 0.04 | 0.03 | 0.02 | 0.02 | 0.02 | 0.03 | 0.02 | 0.03 | 0.06 | 0.03 | 0.12 | 0.01 | 0.17 | 0.04 | 0.00 | 0.02 | 0.00 | 0.00 | 0.06 | 0.05 | 0.18 | 0.28 | 0.12 | 0.05 | 0.05 | 0.04 | 0.09 | 0.17 | 0.16 | 0.12 | 0.00 | 0.04 | 0.01 | 0.00 | 0.05 | 0.06 | 0.01 | 0.11 | 0.03 | 0.09 | 0.00 | 0.00 | 0.03 | 0.03 |
| AFM | ENSG00000079557 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.00 | 0.18 | 0.01 | 0.00 | 0.00 | 0.00 | 0.07 | 0.08 | 0.02 | 0.24 | 0.01 | 0.10 | 0.01 | 0.22 | 0.02 | 0.08 | 0.01 | 0.02 | 0.01 | 0.05 | 0.01 | 0.00 | 0.01 | 0.05 | 0.08 | 0.00 | 0.03 | 0.03 | 0.00 | 0.02 | 0.02 | 0.00 | 0.00 | 0.16 | 0.02 | 0.31 | 0.10 | 0.07 | 0.03 | 0.04 | 0.02 | 0.11 | 0.05 | 0.07 | 0.06 | 0.11 | 0.01 | 0.01 | 0.01 | 0.00 | 0.03 | 0.00 | 0.03 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.03 |
| MOXD1 | ENSG00000079931 | 0.00 | 0.05 | 0.00 | 0.00 | 0.00 | 0.05 | 0.01 | 0.01 | 0.07 | 0.06 | 0.00 | 0.01 | 0.00 | 0.15 | 0.03 | 0.04 | 0.06 | 0.03 | 0.05 | 0.01 | 0.10 | 0.02 | 0.06 | 0.03 | 0.02 | 0.02 | 0.04 | 0.03 | 0.00 | 0.02 | 0.01 | 0.08 | 0.00 | 0.10 | 0.04 | 0.06 | 0.00 | 0.01 | 0.00 | 0.00 | 0.11 | 0.05 | 0.07 | 0.28 | 0.01 | 0.02 | 0.06 | 0.02 | 0.08 | 0.03 | 0.30 | 0.05 | 0.01 | 0.04 | 0.00 | 0.00 | 0.00 | 0.15 | 0.00 | 0.05 | 0.00 | 0.10 | 0.06 | 0.09 | 0.01 | 0.12 |
| DCT | ENSG00000080166 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.08 | 0.16 | 0.06 | 0.00 | 0.01 | 0.01 | 0.02 | 0.11 | 0.04 | 0.11 | 0.05 | 0.07 | 0.02 | 0.09 | 0.05 | 0.14 | 0.03 | 0.09 | 0.01 | 0.13 | 0.01 | 0.02 | 0.02 | 0.25 | 0.04 | 0.06 | 0.03 | 0.03 | 0.01 | 0.02 | 0.00 | 0.00 | 0.00 | 0.13 | 0.04 | 0.21 | 0.09 | 0.16 | 0.04 | 0.05 | 0.02 | 0.57 | 0.05 | 0.22 | 0.12 | 0.01 | 0.00 | 0.00 | 0.00 | 0.08 | 0.04 | 0.02 | 0.03 | 0.02 | 0.05 | 0.05 | 0.00 | 0.07 | 0.04 |
| SLC35C2 | ENSG00000080189 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.01 | 0.10 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.07 | 0.04 | 0.09 | 0.01 | 0.00 | 0.01 | 0.05 | 0.00 | 0.16 | 0.00 | 0.15 | 0.00 | 0.13 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.16 | 0.02 | 0.22 | 0.04 | 0.02 | 0.05 | 0.09 | 0.01 | 0.37 | 0.00 | 0.12 | 0.04 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.08 | 0.01 |
| EPHA6 | ENSG00000080224 | 0.01 | 0.03 | 0.03 | 0.01 | 0.00 | 0.00 | 0.03 | 0.02 | 0.05 | 0.03 | 0.00 | 0.00 | 0.01 | 0.05 | 0.06 | 0.03 | 0.25 | 0.04 | 0.09 | 0.01 | 0.14 | 0.08 | 0.09 | 0.04 | 0.00 | 0.01 | 0.03 | 0.01 | 0.00 | 0.01 | 0.02 | 0.02 | 0.00 | 0.12 | 0.10 | 0.02 | 0.00 | 0.06 | 0.00 | 0.00 | 0.06 | 0.02 | 0.23 | 0.05 | 0.07 | 0.01 | 0.04 | 0.01 | 0.18 | 0.08 | 0.08 | 0.06 | 0.04 | 0.00 | 0.00 | 0.00 | 0.05 | 0.00 | 0.00 | 0.03 | 0.00 | 0.03 | 0.00 | 0.00 | 0.05 | 0.02 |
| SCTR | ENSG00000080293 | 0.00 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.12 | 0.04 | 0.02 | 0.00 | 0.01 | 0.02 | 0.00 | 0.07 | 0.01 | 0.11 | 0.01 | 0.11 | 0.01 | 0.30 | 0.03 | 0.07 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.01 | 0.03 | 0.04 | 0.00 | 0.01 | 0.06 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.04 | 0.10 | 0.13 | 0.03 | 0.00 | 0.05 | 0.02 | 0.12 | 0.00 | 0.16 | 0.02 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.08 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.00 |
| KCNN2 | ENSG00000080709 | 0.20 | 0.01 | 0.03 | 0.01 | 0.00 | 0.01 | 0.02 | 0.12 | 0.04 | 0.07 | 0.00 | 0.01 | 0.00 | 0.08 | 0.02 | 0.07 | 0.00 | 0.07 | 0.01 | 0.05 | 0.03 | 0.07 | 0.02 | 0.13 | 0.01 | 0.13 | 0.01 | 0.09 | 0.00 | 0.05 | 0.07 | 0.04 | 0.05 | 0.02 | 0.22 | 0.04 | 0.00 | 0.03 | 0.00 | 0.00 | 0.02 | 0.06 | 0.09 | 0.37 | 0.00 | 0.05 | 0.01 | 0.03 | 0.01 | 0.08 | 0.10 | 0.03 | 0.01 | 0.00 | 0.00 | 0.09 | 0.04 | 0.02 | 0.00 | 0.03 | 0.00 | 0.01 | 0.00 | 0.00 | 0.05 | 0.07 |
| MOK | ENSG00000080823 | 0.00 | 0.02 | 0.01 | 0.01 | 0.00 | 0.04 | 0.03 | 0.03 | 0.08 | 0.09 | 0.00 | 0.02 | 0.00 | 0.09 | 0.06 | 0.06 | 0.17 | 0.03 | 0.05 | 0.06 | 0.09 | 0.06 | 0.04 | 0.08 | 0.00 | 0.04 | 0.02 | 0.04 | 0.01 | 0.03 | 0.00 | 0.10 | 0.00 | 0.31 | 0.10 | 0.00 | 0.01 | 0.04 | 0.00 | 0.00 | 0.08 | 0.07 | 0.25 | 0.16 | 0.06 | 0.10 | 0.08 | 0.02 | 0.10 | 0.02 | 0.17 | 0.05 | 0.04 | 0.01 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.08 | 0.03 | 0.06 | 0.03 | 0.01 | 0.01 | 0.06 |
| CXCL2 | ENSG00000081041 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.03 | 0.01 | 0.13 | 0.02 | 0.00 | 0.00 | 0.00 | 0.06 | 0.07 | 0.02 | 0.22 | 0.01 | 0.10 | 0.01 | 0.22 | 0.02 | 0.09 | 0.02 | 0.02 | 0.01 | 0.05 | 0.01 | 0.01 | 0.00 | 0.02 | 0.08 | 0.00 | 0.03 | 0.11 | 0.00 | 0.02 | 0.02 | 0.00 | 0.00 | 0.16 | 0.02 | 0.30 | 0.12 | 0.04 | 0.03 | 0.03 | 0.01 | 0.05 | 0.05 | 0.07 | 0.06 | 0.09 | 0.01 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.03 |
| AFP | ENSG00000081051 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.00 | 0.18 | 0.01 | 0.00 | 0.00 | 0.00 | 0.07 | 0.08 | 0.02 | 0.24 | 0.01 | 0.10 | 0.01 | 0.22 | 0.02 | 0.08 | 0.01 | 0.02 | 0.01 | 0.05 | 0.01 | 0.00 | 0.01 | 0.08 | 0.08 | 0.00 | 0.03 | 0.06 | 0.00 | 0.02 | 0.02 | 0.00 | 0.00 | 0.16 | 0.02 | 0.32 | 0.10 | 0.07 | 0.03 | 0.04 | 0.03 | 0.15 | 0.05 | 0.07 | 0.06 | 0.11 | 0.01 | 0.01 | 0.01 | 0.00 | 0.03 | 0.00 | 0.03 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.03 |
| COL4A4 | ENSG00000081052 | 0.01 | 0.07 | 0.04 | 0.04 | 0.00 | 0.05 | 0.01 | 0.03 | 0.01 | 0.32 | 0.00 | 0.03 | 0.00 | 0.12 | 0.04 | 0.04 | 0.01 | 0.19 | 0.01 | 0.18 | 0.06 | 0.14 | 0.05 | 0.04 | 0.02 | 0.03 | 0.02 | 0.02 | 0.09 | 0.02 | 0.04 | 0.05 | 0.00 | 0.04 | 0.03 | 0.03 | 0.01 | 0.01 | 0.00 | 0.01 | 0.03 | 0.08 | 0.15 | 0.19 | 0.01 | 0.37 | 0.02 | 0.05 | 0.16 | 0.06 | 0.10 | 0.22 | 0.06 | 0.02 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.04 | 0.00 | 0.01 | 0.02 | 0.05 | 0.03 | 0.06 |
| SLC13A1 | ENSG00000081800 | 0.01 | 0.01 | 0.08 | 0.01 | 0.01 | 0.00 | 0.01 | 0.04 | 0.04 | 0.04 | 0.00 | 0.01 | 0.04 | 0.07 | 0.07 | 0.03 | 0.08 | 0.06 | 0.03 | 0.10 | 0.03 | 0.17 | 0.06 | 0.06 | 0.01 | 0.00 | 0.00 | 0.02 | 0.01 | 0.04 | 0.08 | 0.05 | 0.00 | 0.02 | 0.00 | 0.06 | 0.01 | 0.02 | 0.00 | 0.00 | 0.06 | 0.04 | 0.28 | 0.06 | 0.04 | 0.06 | 0.02 | 0.05 | 0.05 | 0.12 | 0.19 | 0.03 | 0.03 | 0.02 | 0.00 | 0.03 | 0.09 | 0.07 | 0.10 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.17 | 0.01 |
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