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 |
| LECT1 | ENSG00000136110 | 0.00 | 0.02 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.32 | 0.03 | 0.22 | 0.00 | 0.00 | 0.00 | 0.14 | 0.04 | 0.06 | 0.02 | 0.12 | 0.02 | 0.10 | 0.11 | 0.06 | 0.12 | 0.03 | 0.10 | 0.02 | 0.12 | 0.04 | 0.01 | 0.01 | 0.01 | 0.26 | 0.00 | 0.03 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.02 | 0.03 | 0.11 | 0.06 | 0.21 | 0.02 | 0.19 | 0.00 | 0.03 | 0.03 | 0.12 | 0.03 | 0.33 | 0.03 | 0.02 | 0.00 | 0.00 | 0.03 | 0.06 | 0.00 | 0.09 | 0.01 | 0.16 | 0.00 | 0.00 | 0.01 | 0.04 |
| THSD1 | ENSG00000136114 | 0.00 | 0.02 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.32 | 0.03 | 0.23 | 0.00 | 0.00 | 0.00 | 0.14 | 0.04 | 0.06 | 0.02 | 0.10 | 0.01 | 0.10 | 0.11 | 0.06 | 0.13 | 0.03 | 0.10 | 0.02 | 0.11 | 0.04 | 0.01 | 0.01 | 0.01 | 0.26 | 0.00 | 0.03 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.02 | 0.02 | 0.12 | 0.06 | 0.21 | 0.02 | 0.19 | 0.00 | 0.03 | 0.03 | 0.12 | 0.01 | 0.33 | 0.03 | 0.02 | 0.00 | 0.00 | 0.03 | 0.06 | 0.00 | 0.09 | 0.01 | 0.17 | 0.00 | 0.00 | 0.03 | 0.04 |
| ITM2B | ENSG00000136156 | 0.00 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.39 | 0.03 | 0.29 | 0.00 | 0.00 | 0.00 | 0.16 | 0.01 | 0.08 | 0.01 | 0.15 | 0.01 | 0.14 | 0.03 | 0.10 | 0.10 | 0.05 | 0.10 | 0.03 | 0.10 | 0.04 | 0.01 | 0.01 | 0.00 | 0.31 | 0.00 | 0.09 | 0.00 | 0.12 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.16 | 0.03 | 0.33 | 0.00 | 0.24 | 0.00 | 0.05 | 0.03 | 0.27 | 0.00 | 0.57 | 0.00 | 0.02 | 0.00 | 0.00 | 0.03 | 0.12 | 0.00 | 0.08 | 0.00 | 0.15 | 0.00 | 0.00 | 0.02 | 0.04 |
| EDNRB | ENSG00000136160 | 0.01 | 0.01 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.21 | 0.15 | 0.10 | 0.00 | 0.02 | 0.00 | 0.06 | 0.07 | 0.05 | 0.06 | 0.07 | 0.09 | 0.05 | 0.05 | 0.05 | 0.11 | 0.03 | 0.10 | 0.01 | 0.18 | 0.02 | 0.01 | 0.00 | 0.10 | 0.11 | 0.00 | 0.03 | 0.00 | 0.03 | 0.00 | 0.06 | 0.00 | 0.01 | 0.06 | 0.06 | 0.14 | 0.11 | 0.15 | 0.05 | 0.03 | 0.03 | 0.27 | 0.05 | 0.13 | 0.18 | 0.00 | 0.04 | 0.00 | 0.02 | 0.04 | 0.04 | 0.00 | 0.06 | 0.01 | 0.09 | 0.05 | 0.00 | 0.06 | 0.02 |
| IL6 | ENSG00000136244 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 | 0.09 | 0.01 | 0.00 | 0.00 | 0.03 | 0.00 | 0.14 | 0.00 | 0.15 | 0.01 | 0.05 | 0.01 | 0.20 | 0.01 | 0.09 | 0.02 | 0.05 | 0.00 | 0.03 | 0.00 | 0.02 | 0.00 | 0.05 | 0.00 | 0.00 | 0.01 | 0.06 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.11 | 0.03 | 0.20 | 0.20 | 0.04 | 0.00 | 0.07 | 0.03 | 0.22 | 0.01 | 0.14 | 0.04 | 0.06 | 0.01 | 0.00 | 0.02 | 0.17 | 0.02 | 0.00 | 0.00 | 0.04 | 0.01 | 0.00 | 0.00 | 0.08 | 0.02 |
| ALPK3 | ENSG00000136383 | 0.00 | 0.00 | 0.01 | 0.00 | 0.02 | 0.02 | 0.02 | 0.02 | 0.04 | 0.02 | 0.03 | 0.00 | 0.11 | 0.00 | 0.03 | 0.02 | 0.15 | 0.01 | 0.04 | 0.02 | 0.18 | 0.01 | 0.12 | 0.01 | 0.04 | 0.01 | 0.03 | 0.00 | 0.05 | 0.01 | 0.06 | 0.03 | 0.05 | 0.01 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.15 | 0.02 | 0.25 | 0.08 | 0.16 | 0.00 | 0.03 | 0.03 | 0.28 | 0.05 | 0.10 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.06 | 0.00 | 0.01 | 0.01 | 0.01 | 0.02 | 0.00 | 0.00 | 0.16 | 0.01 |
| CHAD | ENSG00000136457 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.14 | 0.01 | 0.01 | 0.01 | 0.09 | 0.00 | 0.09 | 0.00 | 0.11 | 0.01 | 0.02 | 0.01 | 0.15 | 0.01 | 0.11 | 0.01 | 0.03 | 0.01 | 0.07 | 0.04 | 0.06 | 0.02 | 0.06 | 0.01 | 0.02 | 0.01 | 0.07 | 0.03 | 0.02 | 0.03 | 0.00 | 0.00 | 0.51 | 0.03 | 0.17 | 0.03 | 0.07 | 0.00 | 0.10 | 0.02 | 0.35 | 0.00 | 0.08 | 0.04 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.03 | 0.01 | 0.03 | 0.03 | 0.14 | 0.01 |
| CSH1 | ENSG00000136488 | 0.02 | 0.00 | 0.05 | 0.00 | 0.00 | 0.00 | 0.03 | 0.02 | 0.25 | 0.01 | 0.02 | 0.00 | 0.12 | 0.00 | 0.15 | 0.01 | 0.20 | 0.01 | 0.07 | 0.02 | 0.21 | 0.02 | 0.11 | 0.02 | 0.07 | 0.01 | 0.07 | 0.02 | 0.08 | 0.10 | 0.20 | 0.00 | 0.12 | 0.01 | 0.15 | 0.03 | 0.02 | 0.00 | 0.00 | 0.00 | 0.57 | 0.01 | 0.24 | 0.03 | 0.17 | 0.02 | 0.10 | 0.03 | 0.27 | 0.02 | 0.17 | 0.03 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.02 | 0.06 | 0.00 | 0.03 | 0.01 | 0.16 | 0.00 | 0.24 | 0.01 |
| EPRS | ENSG00000136628 | 0.01 | 0.02 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.06 | 0.09 | 0.06 | 0.02 | 0.02 | 0.05 | 0.01 | 0.08 | 0.01 | 0.12 | 0.01 | 0.05 | 0.00 | 0.20 | 0.03 | 0.06 | 0.01 | 0.02 | 0.00 | 0.06 | 0.02 | 0.00 | 0.01 | 0.15 | 0.02 | 0.16 | 0.02 | 0.08 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.22 | 0.02 | 0.28 | 0.12 | 0.06 | 0.01 | 0.07 | 0.02 | 0.16 | 0.00 | 0.04 | 0.21 | 0.02 | 0.03 | 0.01 | 0.00 | 0.07 | 0.07 | 0.00 | 0.02 | 0.01 | 0.06 | 0.09 | 0.00 | 0.11 | 0.03 |
| IL10 | ENSG00000136634 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.02 | 0.07 | 0.06 | 0.01 | 0.00 | 0.07 | 0.01 | 0.12 | 0.01 | 0.09 | 0.01 | 0.05 | 0.00 | 0.17 | 0.06 | 0.10 | 0.01 | 0.04 | 0.00 | 0.12 | 0.02 | 0.00 | 0.00 | 0.19 | 0.01 | 0.18 | 0.02 | 0.01 | 0.03 | 0.01 | 0.00 | 0.00 | 0.00 | 0.28 | 0.01 | 0.21 | 0.11 | 0.07 | 0.00 | 0.07 | 0.02 | 0.20 | 0.04 | 0.04 | 0.18 | 0.03 | 0.02 | 0.01 | 0.00 | 0.16 | 0.10 | 0.00 | 0.01 | 0.04 | 0.02 | 0.09 | 0.00 | 0.15 | 0.02 |
| IL36G | ENSG00000136688 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.04 | 0.05 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.01 | 0.09 | 0.01 | 0.09 | 0.01 | 0.21 | 0.02 | 0.08 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.01 | 0.03 | 0.00 | 0.01 | 0.05 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.03 | 0.19 | 0.11 | 0.05 | 0.02 | 0.18 | 0.01 | 0.21 | 0.00 | 0.11 | 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 | 0.01 | 0.01 |
| IL1RN | ENSG00000136689 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.04 | 0.05 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 | 0.10 | 0.01 | 0.08 | 0.01 | 0.20 | 0.02 | 0.08 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.01 | 0.03 | 0.00 | 0.01 | 0.05 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.03 | 0.23 | 0.10 | 0.05 | 0.02 | 0.23 | 0.01 | 0.34 | 0.00 | 0.11 | 0.01 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.08 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.01 |
| IL36RN | ENSG00000136695 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.04 | 0.05 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.01 | 0.09 | 0.01 | 0.08 | 0.01 | 0.20 | 0.02 | 0.08 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.02 | 0.02 | 0.00 | 0.01 | 0.05 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.03 | 0.22 | 0.10 | 0.05 | 0.02 | 0.19 | 0.01 | 0.24 | 0.00 | 0.11 | 0.01 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.08 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.01 |
| IL36B | ENSG00000136696 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.04 | 0.05 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.01 | 0.09 | 0.01 | 0.08 | 0.01 | 0.21 | 0.02 | 0.09 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.02 | 0.03 | 0.00 | 0.01 | 0.05 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.03 | 0.22 | 0.10 | 0.05 | 0.02 | 0.19 | 0.01 | 0.21 | 0.00 | 0.11 | 0.01 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.08 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.01 |
| IL1F10 | ENSG00000136697 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.04 | 0.05 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.01 | 0.09 | 0.01 | 0.08 | 0.01 | 0.20 | 0.02 | 0.08 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.02 | 0.02 | 0.00 | 0.01 | 0.05 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.03 | 0.22 | 0.10 | 0.05 | 0.02 | 0.20 | 0.01 | 0.24 | 0.00 | 0.11 | 0.01 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.08 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.01 |
| CFC1 | ENSG00000136698 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.15 | 0.04 | 0.03 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.01 | 0.06 | 0.02 | 0.04 | 0.01 | 0.08 | 0.05 | 0.04 | 0.04 | 0.01 | 0.01 | 0.00 | 0.01 | 0.02 | 0.01 | 0.01 | 0.03 | 0.00 | 0.03 | 0.05 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.05 | 0.08 | 0.17 | 0.02 | 0.01 | 0.04 | 0.01 | 0.07 | 0.00 | 0.13 | 0.04 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.12 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 |
| SMPD4 | ENSG00000136699 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.15 | 0.05 | 0.03 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.01 | 0.08 | 0.02 | 0.05 | 0.01 | 0.08 | 0.06 | 0.03 | 0.05 | 0.01 | 0.01 | 0.00 | 0.01 | 0.02 | 0.01 | 0.02 | 0.03 | 0.00 | 0.03 | 0.05 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.05 | 0.08 | 0.18 | 0.02 | 0.00 | 0.04 | 0.01 | 0.07 | 0.00 | 0.15 | 0.03 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.12 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 |
| GYPC | ENSG00000136732 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.15 | 0.05 | 0.03 | 0.00 | 0.01 | 0.00 | 0.00 | 0.03 | 0.01 | 0.09 | 0.02 | 0.06 | 0.01 | 0.07 | 0.06 | 0.03 | 0.05 | 0.00 | 0.02 | 0.01 | 0.01 | 0.01 | 0.01 | 0.01 | 0.04 | 0.00 | 0.01 | 0.05 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.05 | 0.09 | 0.17 | 0.03 | 0.00 | 0.03 | 0.01 | 0.07 | 0.00 | 0.15 | 0.02 | 0.03 | 0.01 | 0.00 | 0.00 | 0.00 | 0.12 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 |
| CDK9 | ENSG00000136807 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.05 | 0.00 | 0.03 | 0.02 | 0.00 | 0.01 | 0.00 | 0.02 | 0.04 | 0.02 | 0.06 | 0.02 | 0.06 | 0.01 | 0.12 | 0.02 | 0.10 | 0.01 | 0.01 | 0.01 | 0.04 | 0.02 | 0.00 | 0.01 | 0.05 | 0.03 | 0.07 | 0.04 | 0.14 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.09 | 0.03 | 0.10 | 0.17 | 0.05 | 0.01 | 0.08 | 0.04 | 0.15 | 0.11 | 0.04 | 0.07 | 0.02 | 0.04 | 0.01 | 0.00 | 0.05 | 0.00 | 0.02 | 0.00 | 0.03 | 0.02 | 0.00 | 0.00 | 0.05 | 0.02 |
| TXN | ENSG00000136810 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.03 | 0.01 | 0.04 | 0.04 | 0.00 | 0.00 | 0.02 | 0.02 | 0.05 | 0.03 | 0.05 | 0.01 | 0.05 | 0.00 | 0.08 | 0.02 | 0.03 | 0.04 | 0.00 | 0.02 | 0.05 | 0.02 | 0.00 | 0.01 | 0.02 | 0.05 | 0.00 | 0.11 | 0.06 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.05 | 0.09 | 0.14 | 0.02 | 0.02 | 0.01 | 0.04 | 0.00 | 0.15 | 0.13 | 0.03 | 0.04 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.03 | 0.01 | 0.00 | 0.01 | 0.03 | 0.01 |
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