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 |
| TNNC1 | ENSG00000114854 | 0.00 | 0.18 | 0.00 | 0.03 | 0.00 | 0.02 | 0.00 | 0.03 | 0.04 | 0.17 | 0.00 | 0.01 | 0.00 | 0.70 | 0.01 | 0.05 | 0.01 | 0.11 | 0.00 | 0.06 | 0.04 | 0.12 | 0.01 | 0.11 | 0.00 | 0.06 | 0.02 | 0.07 | 0.00 | 0.04 | 0.05 | 0.06 | 0.00 | 0.20 | 0.19 | 0.01 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.17 | 0.08 | 0.23 | 0.00 | 0.09 | 0.10 | 0.07 | 0.05 | 0.27 | 0.04 | 0.15 | 0.05 | 0.01 | 0.00 | 0.01 | 0.00 | 0.06 | 0.01 | 0.06 | 0.03 | 0.05 | 0.00 | 0.03 | 0.02 | 0.05 |
| PAOX | ENSG00000148832 | 0.01 | 0.02 | 0.01 | 0.01 | 0.00 | 0.05 | 0.01 | 0.06 | 0.05 | 0.10 | 0.00 | 0.02 | 0.02 | 0.14 | 0.05 | 0.05 | 0.07 | 0.06 | 0.03 | 0.04 | 0.05 | 0.10 | 0.09 | 0.08 | 0.02 | 0.06 | 0.02 | 0.06 | 0.01 | 0.01 | 0.02 | 0.10 | 0.14 | 0.17 | 0.09 | 0.10 | 0.00 | 0.02 | 0.00 | 0.00 | 0.06 | 0.13 | 0.25 | 0.23 | 0.03 | 0.06 | 0.05 | 0.06 | 0.08 | 0.04 | 0.05 | 0.21 | 0.03 | 0.17 | 0.01 | 0.01 | 0.03 | 0.03 | 0.00 | 0.14 | 0.00 | 0.21 | 0.00 | 0.00 | 0.01 | 0.11 |
| MEP1A | ENSG00000112818 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.02 | 0.02 | 0.11 | 0.03 | 0.00 | 0.00 | 0.01 | 0.02 | 0.11 | 0.02 | 0.16 | 0.04 | 0.06 | 0.02 | 0.27 | 0.03 | 0.18 | 0.01 | 0.05 | 0.00 | 0.11 | 0.01 | 0.02 | 0.00 | 0.08 | 0.00 | 0.00 | 0.08 | 0.06 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.10 | 0.03 | 0.23 | 0.07 | 0.06 | 0.03 | 0.06 | 0.01 | 0.03 | 0.03 | 0.10 | 0.03 | 0.02 | 0.01 | 0.00 | 0.00 | 0.09 | 0.02 | 0.01 | 0.00 | 0.00 | 0.02 | 0.02 | 0.00 | 0.06 | 0.01 |
| LAMP3 | ENSG00000078081 | 0.05 | 0.00 | 0.04 | 0.00 | 0.00 | 0.01 | 0.05 | 0.03 | 0.19 | 0.01 | 0.00 | 0.00 | 0.00 | 0.10 | 0.16 | 0.04 | 2.06 | 0.00 | 0.70 | 0.00 | 0.74 | 0.02 | 0.25 | 0.00 | 0.04 | 0.00 | 0.06 | 0.02 | 0.03 | 0.01 | 0.12 | 0.02 | 0.12 | 0.01 | 0.12 | 0.00 | 0.00 | 0.09 | 0.00 | 0.00 | 0.21 | 0.01 | 1.12 | 0.02 | 0.65 | 0.00 | 0.35 | 0.01 | 0.86 | 0.08 | 0.11 | 0.09 | 0.20 | 0.00 | 0.00 | 0.00 | 0.06 | 0.00 | 0.07 | 0.00 | 0.23 | 0.00 | 0.00 | 0.00 | 0.02 | 0.04 |
| DDR2 | ENSG00000162733 | 0.03 | 0.00 | 0.01 | 0.00 | 0.00 | 0.03 | 0.01 | 0.04 | 0.79 | 0.01 | 0.02 | 0.00 | 0.10 | 0.02 | 0.24 | 0.00 | 0.26 | 0.00 | 0.05 | 0.00 | 0.23 | 0.01 | 0.13 | 0.00 | 0.03 | 0.00 | 0.13 | 0.00 | 0.06 | 0.00 | 0.30 | 0.00 | 0.30 | 0.01 | 0.10 | 0.02 | 0.04 | 0.00 | 0.00 | 0.00 | 0.27 | 0.01 | 0.38 | 0.02 | 0.16 | 0.00 | 0.14 | 0.00 | 0.31 | 0.00 | 0.35 | 0.03 | 0.10 | 0.00 | 0.00 | 0.00 | 0.25 | 0.00 | 0.01 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.18 | 0.01 |
| CLCN7 | ENSG00000103249 | 0.01 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 | 0.01 | 0.15 | 0.00 | 0.00 | 0.04 | 0.02 | 0.05 | 0.04 | 0.04 | 0.08 | 0.03 | 0.03 | 0.04 | 0.13 | 0.04 | 0.08 | 0.03 | 0.03 | 0.03 | 0.03 | 0.01 | 0.02 | 0.03 | 0.03 | 0.00 | 0.05 | 0.16 | 0.02 | 0.00 | 0.02 | 0.00 | 0.00 | 0.09 | 0.02 | 0.12 | 0.20 | 0.10 | 0.05 | 0.04 | 0.03 | 0.17 | 0.19 | 0.09 | 0.03 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.04 | 0.01 | 0.00 | 0.02 | 0.02 | 0.00 | 0.00 | 0.04 | 0.02 |
| GCK | ENSG00000106633 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.06 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.01 | 0.09 | 0.02 | 0.03 | 0.01 | 0.10 | 0.03 | 0.05 | 0.01 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.00 | 0.00 | 0.01 | 0.11 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.08 | 0.01 | 0.10 | 0.06 | 0.01 | 0.00 | 0.03 | 0.01 | 0.05 | 0.00 | 0.05 | 0.03 | 0.02 | 0.00 | 0.00 | 0.01 | 0.11 | 0.02 | 0.01 | 0.00 | 0.05 | 0.01 | 0.00 | 0.00 | 0.03 | 0.03 |
| SLC22A17 | ENSG00000092096 | 0.00 | 0.00 | 0.03 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.14 | 0.06 | 0.01 | 0.00 | 0.00 | 0.02 | 0.18 | 0.03 | 0.16 | 0.07 | 0.06 | 0.07 | 0.12 | 0.05 | 0.05 | 0.04 | 0.02 | 0.02 | 0.01 | 0.07 | 0.01 | 0.03 | 0.08 | 0.00 | 0.00 | 0.02 | 0.28 | 0.03 | 0.00 | 0.02 | 0.00 | 0.00 | 0.12 | 0.03 | 0.26 | 0.12 | 0.09 | 0.02 | 0.05 | 0.03 | 0.06 | 0.07 | 0.23 | 0.03 | 0.01 | 0.03 | 0.00 | 0.01 | 0.00 | 0.00 | 0.03 | 0.03 | 0.03 | 0.09 | 0.00 | 0.00 | 0.03 | 0.03 |
| WHSC1L1 | ENSG00000147548 | 0.00 | 0.01 | 0.03 | 0.00 | 0.00 | 0.00 | 0.07 | 0.07 | 0.38 | 0.05 | 0.00 | 0.00 | 0.04 | 0.00 | 0.17 | 0.04 | 1.20 | 0.03 | 0.38 | 0.03 | 0.40 | 0.06 | 0.07 | 0.03 | 0.24 | 0.03 | 0.29 | 0.03 | 0.12 | 0.00 | 0.06 | 0.05 | 0.02 | 0.02 | 0.05 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.73 | 0.04 | 0.24 | 0.10 | 0.06 | 0.03 | 0.15 | 0.06 | 0.69 | 0.11 | 0.26 | 0.04 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.01 | 0.04 | 0.03 |
| CD55 | ENSG00000196352 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.02 | 0.06 | 0.06 | 0.01 | 0.00 | 0.07 | 0.01 | 0.12 | 0.01 | 0.09 | 0.01 | 0.05 | 0.00 | 0.16 | 0.05 | 0.07 | 0.01 | 0.04 | 0.00 | 0.12 | 0.02 | 0.01 | 0.00 | 0.16 | 0.01 | 0.18 | 0.02 | 0.01 | 0.03 | 0.01 | 0.00 | 0.00 | 0.00 | 0.26 | 0.01 | 0.20 | 0.12 | 0.06 | 0.00 | 0.06 | 0.02 | 0.13 | 0.04 | 0.04 | 0.18 | 0.02 | 0.03 | 0.01 | 0.00 | 0.16 | 0.10 | 0.00 | 0.02 | 0.03 | 0.02 | 0.09 | 0.00 | 0.14 | 0.02 |
| CD200R1 | ENSG00000163606 | 0.00 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.03 | 0.05 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.04 | 0.02 | 0.13 | 0.03 | 0.05 | 0.01 | 0.08 | 0.04 | 0.06 | 0.02 | 0.00 | 0.00 | 0.01 | 0.02 | 0.00 | 0.01 | 0.02 | 0.01 | 0.00 | 0.02 | 0.10 | 0.02 | 0.00 | 0.05 | 0.00 | 0.00 | 0.07 | 0.02 | 0.38 | 0.04 | 0.04 | 0.01 | 0.04 | 0.01 | 0.14 | 0.08 | 0.12 | 0.05 | 0.01 | 0.01 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.03 | 0.01 | 0.05 | 0.00 | 0.00 | 0.02 | 0.04 |
| CYP3A4 | ENSG00000160868 | 0.01 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.04 | 0.02 | 0.08 | 0.01 | 0.00 | 0.00 | 0.03 | 0.00 | 0.12 | 0.02 | 0.24 | 0.01 | 0.24 | 0.00 | 0.52 | 0.02 | 0.32 | 0.01 | 0.02 | 0.00 | 0.02 | 0.00 | 0.11 | 0.01 | 0.11 | 0.01 | 0.11 | 0.03 | 0.10 | 0.03 | 0.00 | 0.02 | 0.00 | 0.00 | 0.07 | 0.03 | 0.20 | 0.05 | 0.07 | 0.01 | 0.07 | 0.02 | 0.15 | 0.04 | 0.07 | 0.04 | 0.09 | 0.01 | 0.00 | 0.00 | 0.13 | 0.00 | 0.06 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.04 | 0.03 |
| CAPN5 | ENSG00000149260 | 0.01 | 0.01 | 0.00 | 0.00 | 0.09 | 0.00 | 0.05 | 0.00 | 0.23 | 0.03 | 0.00 | 0.00 | 0.08 | 0.00 | 0.15 | 0.01 | 0.16 | 0.02 | 0.26 | 0.03 | 0.27 | 0.04 | 0.16 | 0.01 | 0.01 | 0.00 | 0.03 | 0.02 | 0.01 | 0.01 | 0.07 | 0.01 | 0.24 | 0.02 | 0.04 | 0.00 | 0.02 | 0.02 | 0.00 | 0.00 | 0.58 | 0.03 | 0.72 | 0.02 | 0.14 | 0.01 | 0.15 | 0.01 | 0.26 | 0.15 | 0.22 | 0.05 | 0.02 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 | 0.01 | 0.00 | 0.00 | 0.33 | 0.00 |
| NRG2 | ENSG00000158458 | 0.30 | 0.00 | 0.03 | 0.01 | 0.02 | 0.00 | 0.03 | 0.02 | 0.02 | 0.04 | 0.00 | 0.00 | 0.00 | 0.04 | 0.01 | 0.04 | 0.03 | 0.03 | 0.01 | 0.03 | 0.06 | 0.03 | 0.02 | 0.05 | 0.01 | 0.02 | 0.02 | 0.02 | 0.02 | 0.01 | 0.10 | 0.02 | 0.09 | 0.01 | 0.38 | 0.02 | 0.00 | 0.05 | 0.01 | 0.00 | 0.04 | 0.02 | 0.15 | 0.12 | 0.03 | 0.01 | 0.06 | 0.02 | 0.17 | 0.01 | 0.06 | 0.04 | 0.00 | 0.00 | 0.00 | 0.10 | 0.04 | 0.00 | 0.01 | 0.05 | 0.02 | 0.02 | 0.00 | 0.03 | 0.04 | 0.14 |
| DYRK1A | ENSG00000157540 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 | 0.07 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.03 | 0.02 | 0.05 | 0.03 | 0.04 | 0.03 | 0.09 | 0.03 | 0.10 | 0.02 | 0.01 | 0.02 | 0.07 | 0.01 | 0.01 | 0.01 | 0.01 | 0.07 | 0.03 | 0.00 | 0.04 | 0.01 | 0.00 | 0.00 | 0.00 | 0.10 | 0.01 | 0.14 | 0.14 | 0.14 | 0.01 | 0.04 | 0.02 | 0.01 | 0.03 | 0.09 | 0.08 | 0.04 | 0.00 | 0.11 | 0.00 | 0.00 | 0.02 | 0.00 | 0.01 | 0.00 | 0.02 | 0.03 | 0.00 | 0.01 | 0.01 |
| LTBP2 | ENSG00000119681 | 0.00 | 0.03 | 0.00 | 0.01 | 0.00 | 0.05 | 0.01 | 0.05 | 0.05 | 0.05 | 0.00 | 0.01 | 0.00 | 0.06 | 0.04 | 0.05 | 0.05 | 0.03 | 0.05 | 0.01 | 0.06 | 0.02 | 0.03 | 0.04 | 0.00 | 0.03 | 0.01 | 0.03 | 0.03 | 0.01 | 0.01 | 0.10 | 0.00 | 0.28 | 0.05 | 0.03 | 0.01 | 0.04 | 0.00 | 0.00 | 0.02 | 0.10 | 0.14 | 0.20 | 0.05 | 0.03 | 0.03 | 0.02 | 0.08 | 0.06 | 0.08 | 0.11 | 0.04 | 0.01 | 0.00 | 0.00 | 0.04 | 0.00 | 0.00 | 0.12 | 0.01 | 0.08 | 0.03 | 0.00 | 0.00 | 0.05 |
| QPCT | ENSG00000115828 | 0.00 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.07 | 0.06 | 0.01 | 0.00 | 0.00 | 0.01 | 0.05 | 0.08 | 0.01 | 0.08 | 0.02 | 0.03 | 0.02 | 0.03 | 0.03 | 0.02 | 0.03 | 0.00 | 0.01 | 0.00 | 0.03 | 0.01 | 0.03 | 0.05 | 0.01 | 0.00 | 0.05 | 0.01 | 0.04 | 0.00 | 0.01 | 0.00 | 0.00 | 0.05 | 0.03 | 0.19 | 0.05 | 0.07 | 0.00 | 0.07 | 0.02 | 0.16 | 0.03 | 0.07 | 0.07 | 0.13 | 0.01 | 0.00 | 0.00 | 0.10 | 0.02 | 0.01 | 0.01 | 0.01 | 0.01 | 0.03 | 0.00 | 0.01 | 0.01 |
| SETD8 | ENSG00000183955 | 0.01 | 0.01 | 0.02 | 0.00 | 0.07 | 0.02 | 0.03 | 0.06 | 0.08 | 0.03 | 0.00 | 0.00 | 0.01 | 0.02 | 0.03 | 0.05 | 0.03 | 0.06 | 0.03 | 0.03 | 0.08 | 0.05 | 0.05 | 0.04 | 0.01 | 0.01 | 0.05 | 0.01 | 0.00 | 0.06 | 0.02 | 0.10 | 0.00 | 0.20 | 0.09 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.06 | 0.09 | 0.15 | 0.23 | 0.02 | 0.02 | 0.06 | 0.07 | 0.21 | 0.16 | 0.20 | 0.06 | 0.01 | 0.00 | 0.00 | 0.01 | 0.07 | 0.03 | 0.04 | 0.01 | 0.02 | 0.00 | 0.00 | 0.00 | 0.04 | 0.07 |
| SLC16A9 | ENSG00000165449 | 0.00 | 0.01 | 0.00 | 0.01 | 0.03 | 0.00 | 0.02 | 0.04 | 0.03 | 0.05 | 0.00 | 0.00 | 0.01 | 0.04 | 0.03 | 0.03 | 0.06 | 0.04 | 0.06 | 0.02 | 0.08 | 0.08 | 0.08 | 0.02 | 0.01 | 0.03 | 0.00 | 0.04 | 0.01 | 0.00 | 0.02 | 0.02 | 0.19 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.12 | 0.03 | 0.14 | 0.10 | 0.02 | 0.01 | 0.08 | 0.03 | 0.44 | 0.03 | 0.02 | 0.08 | 0.00 | 0.01 | 0.00 | 0.00 | 0.03 | 0.00 | 0.01 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.04 |
| PDE12 | ENSG00000174840 | 0.00 | 0.11 | 0.00 | 0.02 | 0.00 | 0.02 | 0.00 | 0.02 | 0.02 | 0.13 | 0.00 | 0.02 | 0.00 | 0.36 | 0.00 | 0.05 | 0.01 | 0.11 | 0.00 | 0.07 | 0.00 | 0.13 | 0.02 | 0.08 | 0.00 | 0.05 | 0.02 | 0.06 | 0.00 | 0.03 | 0.01 | 0.06 | 0.00 | 0.17 | 0.06 | 0.01 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.17 | 0.13 | 0.17 | 0.00 | 0.11 | 0.02 | 0.07 | 0.04 | 0.38 | 0.03 | 0.14 | 0.06 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 | 0.03 | 0.00 | 0.00 | 0.06 | 0.02 |
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