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 |
| TTBK1 | ENSG00000146216 | 0.01 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.02 | 0.01 | 0.17 | 0.02 | 0.00 | 0.00 | 0.00 | 0.02 | 0.11 | 0.01 | 0.16 | 0.04 | 0.07 | 0.02 | 0.55 | 0.02 | 0.36 | 0.00 | 0.10 | 0.00 | 0.21 | 0.00 | 0.04 | 0.00 | 0.14 | 0.00 | 0.05 | 0.02 | 0.06 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.12 | 0.03 | 0.30 | 0.07 | 0.07 | 0.02 | 0.06 | 0.01 | 0.10 | 0.03 | 0.15 | 0.03 | 0.05 | 0.01 | 0.00 | 0.00 | 0.11 | 0.00 | 0.01 | 0.00 | 0.01 | 0.01 | 0.02 | 0.00 | 0.06 | 0.00 |
| VAT1L | ENSG00000171724 | 0.01 | 0.00 | 0.00 | 0.03 | 0.00 | 0.06 | 0.01 | 0.22 | 0.11 | 0.03 | 0.00 | 0.00 | 0.00 | 0.13 | 0.04 | 0.07 | 0.04 | 0.05 | 0.02 | 0.03 | 0.08 | 0.03 | 0.06 | 0.03 | 0.02 | 0.01 | 0.02 | 0.02 | 0.01 | 0.01 | 0.01 | 0.06 | 0.05 | 0.01 | 0.06 | 0.06 | 0.02 | 0.02 | 0.00 | 0.01 | 0.04 | 0.07 | 0.05 | 0.31 | 0.03 | 0.03 | 0.03 | 0.07 | 0.05 | 0.24 | 0.04 | 0.04 | 0.00 | 0.10 | 0.00 | 0.06 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.05 | 0.00 | 0.00 | 0.02 | 0.05 |
| CAPN12 | ENSG00000182472 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.02 | 0.02 | 0.02 | 0.32 | 0.02 | 0.00 | 0.00 | 0.08 | 0.03 | 0.19 | 0.03 | 0.54 | 0.03 | 0.07 | 0.01 | 0.09 | 0.04 | 0.11 | 0.02 | 0.05 | 0.01 | 0.02 | 0.01 | 0.19 | 0.00 | 0.05 | 0.01 | 0.12 | 0.01 | 0.05 | 0.03 | 0.01 | 0.02 | 0.00 | 0.00 | 0.13 | 0.03 | 0.72 | 0.12 | 0.28 | 0.03 | 0.17 | 0.03 | 1.18 | 0.11 | 0.25 | 0.11 | 0.00 | 0.03 | 0.01 | 0.00 | 0.03 | 0.00 | 0.02 | 0.04 | 0.04 | 0.04 | 0.00 | 0.00 | 0.04 | 0.02 |
| LRRN1 | ENSG00000175928 | 0.00 | 0.17 | 0.00 | 0.02 | 0.07 | 0.00 | 0.01 | 0.04 | 0.24 | 0.06 | 0.00 | 0.06 | 0.04 | 0.13 | 0.03 | 0.04 | 0.03 | 0.09 | 0.04 | 0.05 | 0.03 | 0.20 | 0.03 | 0.13 | 0.00 | 0.06 | 0.01 | 0.08 | 0.01 | 0.02 | 0.05 | 0.03 | 0.00 | 0.18 | 0.06 | 0.05 | 0.00 | 0.04 | 0.00 | 0.01 | 0.12 | 0.04 | 0.13 | 0.26 | 0.04 | 0.03 | 0.04 | 0.04 | 0.05 | 0.20 | 0.21 | 0.05 | 0.05 | 0.06 | 0.00 | 0.00 | 0.00 | 0.05 | 0.03 | 0.03 | 0.01 | 0.02 | 0.00 | 0.00 | 0.03 | 0.06 |
| DHRS13 | ENSG00000167536 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.27 | 0.01 | 0.08 | 0.00 | 0.00 | 0.03 | 0.08 | 0.01 | 0.10 | 0.03 | 0.04 | 0.02 | 0.19 | 0.01 | 0.12 | 0.01 | 0.09 | 0.01 | 0.08 | 0.00 | 0.03 | 0.01 | 0.08 | 0.00 | 0.07 | 0.01 | 0.10 | 0.05 | 0.00 | 0.14 | 0.00 | 0.00 | 0.37 | 0.03 | 0.22 | 0.09 | 0.02 | 0.03 | 0.19 | 0.01 | 0.32 | 0.03 | 0.03 | 0.18 | 0.00 | 0.01 | 0.00 | 0.03 | 0.04 | 0.00 | 0.00 | 0.01 | 0.03 | 0.03 | 0.00 | 0.00 | 0.05 | 0.03 |
| PMP22 | ENSG00000109099 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.04 | 0.02 | 0.12 | 0.00 | 0.01 | 0.00 | 0.03 | 0.04 | 0.05 | 0.01 | 0.03 | 0.04 | 0.02 | 0.04 | 0.08 | 0.01 | 0.06 | 0.00 | 0.03 | 0.00 | 0.07 | 0.05 | 0.00 | 0.00 | 0.07 | 0.00 | 0.04 | 0.02 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.03 | 0.06 | 0.02 | 0.16 | 0.01 | 0.05 | 0.01 | 0.07 | 0.15 | 0.19 | 0.62 | 0.04 | 0.01 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.02 | 0.01 | 0.03 |
| FAM3B | ENSG00000183844 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.31 | 0.04 | 0.04 | 0.00 | 0.03 | 0.00 | 0.00 | 0.02 | 0.03 | 0.04 | 0.08 | 0.02 | 0.06 | 0.02 | 0.08 | 0.03 | 0.07 | 0.02 | 0.01 | 0.01 | 0.06 | 0.01 | 0.01 | 0.02 | 0.01 | 0.07 | 0.03 | 0.01 | 0.04 | 0.02 | 0.00 | 0.00 | 0.00 | 0.08 | 0.01 | 0.12 | 0.16 | 0.05 | 0.03 | 0.04 | 0.01 | 0.04 | 0.03 | 0.10 | 0.06 | 0.04 | 0.00 | 0.12 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.03 | 0.00 | 0.01 | 0.02 |
| GPRC5B | ENSG00000167191 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.09 | 0.03 | 0.00 | 0.00 | 0.01 | 0.02 | 0.02 | 0.02 | 0.04 | 0.03 | 0.02 | 0.02 | 0.03 | 0.02 | 0.03 | 0.02 | 0.02 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.02 | 0.01 | 0.00 | 0.01 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.01 | 0.17 | 0.04 | 0.05 | 0.00 | 0.07 | 0.01 | 0.09 | 0.00 | 0.03 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.06 | 0.00 | 0.00 | 0.01 | 0.01 | 0.03 | 0.00 | 0.00 | 0.01 | 0.01 |
| VCAN | ENSG00000038427 | 0.01 | 0.01 | 0.01 | 0.01 | 0.03 | 0.01 | 0.02 | 0.08 | 0.02 | 0.09 | 0.00 | 0.01 | 0.00 | 0.03 | 0.02 | 0.07 | 0.01 | 0.09 | 0.01 | 0.08 | 0.01 | 0.12 | 0.00 | 0.12 | 0.00 | 0.07 | 0.01 | 0.02 | 0.00 | 0.09 | 0.02 | 0.03 | 0.00 | 0.08 | 0.07 | 0.03 | 0.00 | 0.04 | 0.00 | 0.00 | 0.01 | 0.07 | 0.03 | 0.65 | 0.00 | 0.06 | 0.00 | 0.09 | 0.00 | 0.21 | 0.03 | 0.04 | 0.00 | 0.00 | 0.00 | 0.04 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.07 | 0.03 |
| DCN | ENSG00000011465 | 0.01 | 0.01 | 0.00 | 0.00 | 0.06 | 0.02 | 0.04 | 0.00 | 0.08 | 0.04 | 0.00 | 0.00 | 0.01 | 0.03 | 0.02 | 0.05 | 0.05 | 0.03 | 0.01 | 0.03 | 0.03 | 0.06 | 0.03 | 0.03 | 0.00 | 0.03 | 0.03 | 0.06 | 0.00 | 0.08 | 0.02 | 0.02 | 0.00 | 0.17 | 0.02 | 0.02 | 0.00 | 0.02 | 0.00 | 0.00 | 0.10 | 0.05 | 0.06 | 0.23 | 0.02 | 0.02 | 0.02 | 0.03 | 0.00 | 0.16 | 0.29 | 0.04 | 0.00 | 0.01 | 0.00 | 0.02 | 0.08 | 0.05 | 0.00 | 0.02 | 0.00 | 0.04 | 0.00 | 0.00 | 0.01 | 0.08 |
| WFDC3 | ENSG00000124116 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.01 | 0.09 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.06 | 0.05 | 0.07 | 0.01 | 0.01 | 0.01 | 0.05 | 0.00 | 0.19 | 0.00 | 0.18 | 0.00 | 0.13 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.00 | 0.01 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.14 | 0.02 | 0.23 | 0.04 | 0.02 | 0.04 | 0.08 | 0.01 | 0.42 | 0.00 | 0.10 | 0.03 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.05 | 0.01 |
| SLC35F1 | ENSG00000196376 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.24 | 0.03 | 0.12 | 0.00 | 0.01 | 0.02 | 0.16 | 0.01 | 0.06 | 0.03 | 0.04 | 0.03 | 0.02 | 0.13 | 0.05 | 0.04 | 0.05 | 0.01 | 0.04 | 0.01 | 0.03 | 0.00 | 0.03 | 0.02 | 0.07 | 0.00 | 0.18 | 0.14 | 0.04 | 0.01 | 0.00 | 0.00 | 0.00 | 0.10 | 0.07 | 0.08 | 0.26 | 0.01 | 0.02 | 0.06 | 0.03 | 0.07 | 0.05 | 0.25 | 0.07 | 0.00 | 0.03 | 0.00 | 0.00 | 0.01 | 0.21 | 0.00 | 0.05 | 0.00 | 0.09 | 0.05 | 0.03 | 0.01 | 0.13 |
| MRGPRF | ENSG00000172935 | 0.01 | 0.00 | 0.03 | 0.01 | 0.08 | 0.02 | 0.09 | 0.00 | 0.48 | 0.02 | 0.00 | 0.00 | 0.08 | 0.00 | 0.21 | 0.01 | 0.70 | 0.01 | 1.19 | 0.01 | 1.79 | 0.02 | 0.26 | 0.03 | 0.02 | 0.02 | 0.07 | 0.02 | 0.04 | 0.01 | 0.37 | 0.01 | 0.69 | 0.05 | 0.00 | 0.01 | 0.03 | 0.00 | 0.00 | 0.00 | 0.85 | 0.02 | 0.37 | 0.04 | 0.23 | 0.01 | 0.12 | 0.01 | 0.33 | 0.06 | 0.16 | 0.05 | 0.00 | 0.05 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.01 | 0.01 | 0.03 | 0.00 | 0.00 | 0.35 | 0.02 |
| ITPR1 | ENSG00000150995 | 0.00 | 0.18 | 0.00 | 0.02 | 0.07 | 0.00 | 0.01 | 0.05 | 0.28 | 0.06 | 0.00 | 0.05 | 0.04 | 0.11 | 0.03 | 0.06 | 0.03 | 0.08 | 0.04 | 0.04 | 0.03 | 0.14 | 0.04 | 0.12 | 0.00 | 0.05 | 0.01 | 0.08 | 0.01 | 0.02 | 0.07 | 0.03 | 0.06 | 0.18 | 0.07 | 0.05 | 0.00 | 0.04 | 0.00 | 0.00 | 0.16 | 0.04 | 0.16 | 0.25 | 0.04 | 0.02 | 0.06 | 0.03 | 0.09 | 0.19 | 0.23 | 0.04 | 0.05 | 0.06 | 0.00 | 0.00 | 0.00 | 0.05 | 0.03 | 0.02 | 0.02 | 0.02 | 0.00 | 0.00 | 0.02 | 0.07 |
| TGFBR3 | ENSG00000069702 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.07 | 0.05 | 0.08 | 0.00 | 0.00 | 0.00 | 0.39 | 0.05 | 0.09 | 0.05 | 0.06 | 0.01 | 0.08 | 0.00 | 0.09 | 0.01 | 0.07 | 0.00 | 0.07 | 0.01 | 0.05 | 0.00 | 0.01 | 0.03 | 0.03 | 0.00 | 0.10 | 0.02 | 0.05 | 0.00 | 0.23 | 0.00 | 0.00 | 0.05 | 0.10 | 0.16 | 0.18 | 0.00 | 0.05 | 0.01 | 0.03 | 0.05 | 0.06 | 0.08 | 0.08 | 0.04 | 0.06 | 0.01 | 0.00 | 0.00 | 0.03 | 0.01 | 0.01 | 0.01 | 0.06 | 0.00 | 0.05 | 0.04 | 0.12 |
| LAMA5 | ENSG00000130702 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.04 | 0.01 | 0.06 | 0.04 | 0.00 | 0.01 | 0.03 | 0.00 | 0.28 | 0.01 | 0.08 | 0.04 | 0.02 | 0.02 | 0.15 | 0.01 | 0.18 | 0.00 | 0.09 | 0.00 | 0.12 | 0.01 | 0.03 | 0.00 | 0.13 | 0.00 | 0.00 | 0.01 | 0.09 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.34 | 0.02 | 0.52 | 0.04 | 0.04 | 0.03 | 0.17 | 0.01 | 0.43 | 0.00 | 0.24 | 0.07 | 0.02 | 0.02 | 0.03 | 0.00 | 0.07 | 0.00 | 0.02 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.11 | 0.00 |
| B2M | ENSG00000166710 | 0.00 | 0.01 | 0.00 | 0.03 | 0.14 | 0.00 | 0.01 | 0.05 | 0.02 | 0.05 | 0.00 | 0.00 | 0.04 | 0.31 | 0.01 | 0.10 | 0.01 | 0.12 | 0.02 | 0.05 | 0.05 | 0.05 | 0.01 | 0.08 | 0.01 | 0.09 | 0.00 | 0.06 | 0.00 | 0.03 | 0.01 | 0.02 | 0.00 | 0.03 | 0.03 | 0.08 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.10 | 0.05 | 0.30 | 0.01 | 0.10 | 0.00 | 0.07 | 0.05 | 0.33 | 0.07 | 0.08 | 0.01 | 0.03 | 0.00 | 0.00 | 0.02 | 0.26 | 0.00 | 0.03 | 0.00 | 0.11 | 0.00 | 0.00 | 0.01 | 0.17 |
| RABGGTB | ENSG00000137955 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.08 | 0.11 | 0.05 | 0.00 | 0.00 | 0.00 | 0.20 | 0.04 | 0.07 | 0.07 | 0.06 | 0.02 | 0.06 | 0.01 | 0.09 | 0.02 | 0.06 | 0.00 | 0.08 | 0.03 | 0.06 | 0.00 | 0.01 | 0.01 | 0.03 | 0.00 | 0.08 | 0.04 | 0.04 | 0.00 | 0.20 | 0.00 | 0.00 | 0.05 | 0.07 | 0.13 | 0.16 | 0.03 | 0.03 | 0.01 | 0.02 | 0.07 | 0.06 | 0.20 | 0.04 | 0.04 | 0.02 | 0.02 | 0.01 | 0.00 | 0.03 | 0.00 | 0.01 | 0.01 | 0.04 | 0.03 | 0.05 | 0.03 | 0.08 |
| TESK2 | ENSG00000070759 | 0.00 | 0.02 | 0.01 | 0.03 | 0.00 | 0.00 | 0.00 | 0.02 | 0.10 | 0.03 | 0.00 | 0.00 | 0.08 | 0.03 | 0.09 | 0.03 | 0.08 | 0.02 | 0.07 | 0.02 | 0.07 | 0.01 | 0.05 | 0.03 | 0.02 | 0.02 | 0.02 | 0.01 | 0.01 | 0.01 | 0.02 | 0.09 | 0.00 | 0.23 | 0.02 | 0.03 | 0.01 | 0.11 | 0.00 | 0.00 | 0.06 | 0.05 | 0.42 | 0.06 | 0.09 | 0.00 | 0.07 | 0.01 | 0.11 | 0.03 | 0.11 | 0.04 | 0.07 | 0.04 | 0.02 | 0.00 | 0.00 | 0.03 | 0.00 | 0.01 | 0.02 | 0.00 | 0.00 | 0.07 | 0.04 | 0.02 |
| SLC12A5 | ENSG00000124140 | 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 | 0.06 | 0.05 | 0.08 | 0.01 | 0.00 | 0.01 | 0.06 | 0.00 | 0.18 | 0.00 | 0.16 | 0.00 | 0.13 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 | 0.00 | 0.01 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.15 | 0.02 | 0.22 | 0.04 | 0.02 | 0.05 | 0.09 | 0.01 | 0.42 | 0.00 | 0.10 | 0.03 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.07 | 0.01 |
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