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 |
| MPZ | ENSG00000158887 | 0.03 | 0.00 | 0.01 | 0.01 | 0.00 | 0.03 | 0.02 | 0.05 | 0.94 | 0.00 | 0.02 | 0.00 | 0.10 | 0.01 | 0.26 | 0.00 | 0.27 | 0.00 | 0.06 | 0.00 | 0.36 | 0.01 | 0.14 | 0.00 | 0.03 | 0.00 | 0.14 | 0.00 | 0.06 | 0.00 | 0.31 | 0.00 | 0.30 | 0.01 | 0.16 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.32 | 0.00 | 0.37 | 0.02 | 0.17 | 0.00 | 0.15 | 0.00 | 0.41 | 0.00 | 0.39 | 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 | 0.17 | 0.01 |
| IFNAR2 | ENSG00000159110 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.07 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 | 0.02 | 0.04 | 0.03 | 0.05 | 0.02 | 0.03 | 0.00 | 0.06 | 0.01 | 0.02 | 0.02 | 0.00 | 0.02 | 0.03 | 0.00 | 0.04 | 0.01 | 0.05 | 0.03 | 0.13 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.01 | 0.12 | 0.05 | 0.02 | 0.01 | 0.03 | 0.00 | 0.04 | 0.03 | 0.08 | 0.04 | 0.02 | 0.00 | 0.05 | 0.01 | 0.00 | 0.00 | 0.02 | 0.02 | 0.01 | 0.02 | 0.03 | 0.00 | 0.01 | 0.01 |
| SV2A | ENSG00000159164 | 0.03 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.06 | 0.03 | 0.51 | 0.04 | 0.02 | 0.00 | 0.10 | 0.13 | 0.39 | 0.12 | 0.28 | 0.13 | 0.10 | 0.16 | 0.23 | 0.11 | 0.19 | 0.04 | 0.03 | 0.04 | 0.16 | 0.03 | 0.05 | 0.01 | 0.35 | 0.03 | 0.43 | 0.01 | 0.22 | 0.03 | 0.10 | 0.26 | 0.00 | 0.00 | 0.37 | 0.05 | 0.62 | 0.09 | 0.16 | 0.06 | 0.26 | 0.02 | 0.50 | 0.04 | 0.44 | 0.12 | 0.12 | 0.03 | 0.00 | 0.00 | 0.28 | 0.02 | 0.01 | 0.01 | 0.03 | 0.03 | 0.00 | 0.03 | 0.19 | 0.05 |
| LAD1 | ENSG00000159166 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.08 | 0.07 | 0.02 | 0.00 | 0.10 | 0.00 | 0.14 | 0.00 | 0.08 | 0.01 | 0.06 | 0.01 | 0.14 | 0.05 | 0.04 | 0.01 | 0.04 | 0.01 | 0.07 | 0.04 | 0.00 | 0.00 | 0.18 | 0.01 | 0.18 | 0.02 | 0.05 | 0.04 | 0.02 | 0.00 | 0.00 | 0.00 | 0.22 | 0.01 | 0.30 | 0.06 | 0.06 | 0.00 | 0.08 | 0.02 | 0.18 | 0.03 | 0.10 | 0.12 | 0.07 | 0.00 | 0.01 | 0.00 | 0.26 | 0.02 | 0.01 | 0.01 | 0.03 | 0.01 | 0.06 | 0.00 | 0.21 | 0.01 |
| STC1 | ENSG00000159167 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.22 | 0.01 | 0.14 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 | 0.07 | 0.00 | 0.10 | 0.00 | 0.06 | 0.01 | 0.06 | 0.01 | 0.04 | 0.00 | 0.10 | 0.01 | 0.20 | 0.00 | 0.05 | 0.00 | 0.12 | 0.00 | 0.05 | 0.02 | 0.00 | 0.02 | 0.03 | 0.00 | 0.00 | 0.01 | 0.16 | 0.01 | 0.45 | 0.00 | 0.05 | 0.01 | 0.12 | 0.00 | 0.24 | 0.02 | 0.07 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.11 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.01 | 0.02 | 0.05 |
| GIP | ENSG00000159224 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.09 | 0.01 | 0.00 | 0.00 | 0.09 | 0.00 | 0.08 | 0.01 | 0.09 | 0.01 | 0.02 | 0.01 | 0.12 | 0.03 | 0.08 | 0.01 | 0.04 | 0.01 | 0.06 | 0.03 | 0.04 | 0.02 | 0.05 | 0.01 | 0.02 | 0.01 | 0.01 | 0.04 | 0.01 | 0.05 | 0.00 | 0.00 | 0.44 | 0.04 | 0.17 | 0.05 | 0.06 | 0.00 | 0.06 | 0.04 | 0.33 | 0.04 | 0.10 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.01 | 0.01 | 0.03 | 0.03 | 0.12 | 0.02 |
| CBR1 | ENSG00000159228 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 | 0.08 | 0.03 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 | 0.03 | 0.02 | 0.05 | 0.02 | 0.03 | 0.03 | 0.04 | 0.04 | 0.05 | 0.02 | 0.02 | 0.04 | 0.05 | 0.01 | 0.01 | 0.01 | 0.01 | 0.05 | 0.03 | 0.08 | 0.04 | 0.01 | 0.00 | 0.00 | 0.00 | 0.06 | 0.02 | 0.11 | 0.08 | 0.10 | 0.01 | 0.02 | 0.01 | 0.00 | 0.03 | 0.04 | 0.07 | 0.03 | 0.00 | 0.07 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.02 | 0.03 | 0.00 | 0.01 | 0.01 |
| ATP13A2 | ENSG00000159363 | 0.00 | 0.06 | 0.01 | 0.08 | 0.00 | 0.00 | 0.00 | 0.04 | 0.07 | 0.08 | 0.00 | 0.01 | 0.04 | 0.26 | 0.07 | 0.06 | 0.04 | 0.11 | 0.03 | 0.09 | 0.07 | 0.09 | 0.06 | 0.09 | 0.00 | 0.16 | 0.00 | 0.21 | 0.02 | 0.06 | 0.03 | 0.23 | 0.00 | 1.11 | 0.03 | 0.07 | 0.01 | 0.09 | 0.00 | 0.00 | 0.02 | 0.21 | 0.13 | 0.42 | 0.04 | 0.08 | 0.06 | 0.13 | 0.03 | 0.25 | 0.19 | 0.17 | 0.05 | 0.08 | 0.02 | 0.00 | 0.00 | 0.07 | 0.00 | 0.02 | 0.04 | 0.08 | 0.00 | 0.07 | 0.07 | 0.09 |
| PSMB4 | ENSG00000159377 | 0.03 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.07 | 0.00 | 0.57 | 0.01 | 0.02 | 0.00 | 0.11 | 0.02 | 0.41 | 0.00 | 0.30 | 0.00 | 0.07 | 0.01 | 0.27 | 0.00 | 0.23 | 0.01 | 0.03 | 0.00 | 0.17 | 0.00 | 0.06 | 0.00 | 0.35 | 0.00 | 0.43 | 0.01 | 0.20 | 0.00 | 0.10 | 0.00 | 0.00 | 0.00 | 0.36 | 0.01 | 0.70 | 0.02 | 0.22 | 0.00 | 0.31 | 0.00 | 0.71 | 0.00 | 0.48 | 0.02 | 0.12 | 0.01 | 0.00 | 0.00 | 0.24 | 0.04 | 0.02 | 0.00 | 0.06 | 0.00 | 0.00 | 0.00 | 0.21 | 0.00 |
| CES5A | ENSG00000159398 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.05 | 0.01 | 0.05 | 0.00 | 0.00 | 0.00 | 0.03 | 0.04 | 0.04 | 0.04 | 0.02 | 0.03 | 0.03 | 0.10 | 0.01 | 0.02 | 0.04 | 0.04 | 0.00 | 0.00 | 0.02 | 0.01 | 0.00 | 0.02 | 0.03 | 0.00 | 0.01 | 0.06 | 0.09 | 0.00 | 0.02 | 0.00 | 0.00 | 0.05 | 0.04 | 0.04 | 0.14 | 0.00 | 0.08 | 0.03 | 0.06 | 0.05 | 0.12 | 0.01 | 0.07 | 0.12 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.03 | 0.00 | 0.05 |
| C1R | ENSG00000159403 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |
| ALDH4A1 | ENSG00000159423 | 0.00 | 0.06 | 0.00 | 0.08 | 0.00 | 0.00 | 0.01 | 0.05 | 0.08 | 0.08 | 0.00 | 0.01 | 0.04 | 0.25 | 0.04 | 0.06 | 0.04 | 0.11 | 0.03 | 0.08 | 0.07 | 0.09 | 0.06 | 0.10 | 0.00 | 0.16 | 0.00 | 0.22 | 0.02 | 0.07 | 0.03 | 0.21 | 0.00 | 1.11 | 0.01 | 0.07 | 0.01 | 0.10 | 0.00 | 0.00 | 0.01 | 0.20 | 0.10 | 0.44 | 0.04 | 0.08 | 0.07 | 0.13 | 0.07 | 0.19 | 0.19 | 0.11 | 0.05 | 0.07 | 0.02 | 0.01 | 0.00 | 0.03 | 0.00 | 0.02 | 0.05 | 0.07 | 0.00 | 0.12 | 0.07 | 0.10 |
| PGLYRP3 | ENSG00000159527 | 0.03 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.06 | 0.00 | 0.48 | 0.01 | 0.02 | 0.00 | 0.11 | 0.00 | 0.38 | 0.00 | 0.29 | 0.00 | 0.05 | 0.01 | 0.24 | 0.01 | 0.18 | 0.00 | 0.02 | 0.00 | 0.17 | 0.00 | 0.06 | 0.00 | 0.35 | 0.00 | 0.49 | 0.01 | 0.14 | 0.02 | 0.10 | 0.00 | 0.00 | 0.00 | 0.33 | 0.00 | 0.54 | 0.02 | 0.20 | 0.00 | 0.18 | 0.00 | 0.61 | 0.00 | 0.43 | 0.01 | 0.12 | 0.00 | 0.00 | 0.00 | 0.20 | 0.04 | 0.01 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.21 | 0.00 |
| ATP6V0D1 | ENSG00000159720 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.06 | 0.00 | 0.06 | 0.15 | 0.02 | 0.00 | 0.00 | 0.03 | 0.06 | 0.04 | 0.03 | 0.05 | 0.01 | 0.03 | 0.01 | 0.12 | 0.01 | 0.05 | 0.03 | 0.00 | 0.00 | 0.01 | 0.01 | 0.01 | 0.00 | 0.01 | 0.04 | 0.05 | 0.01 | 0.28 | 0.03 | 0.01 | 0.02 | 0.00 | 0.01 | 0.02 | 0.05 | 0.04 | 0.31 | 0.03 | 0.03 | 0.02 | 0.08 | 0.05 | 0.18 | 0.02 | 0.04 | 0.15 | 0.01 | 0.00 | 0.05 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 | 0.00 | 0.03 | 0.05 | 0.00 |
| AGRP | ENSG00000159723 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.06 | 0.00 | 0.06 | 0.14 | 0.02 | 0.00 | 0.00 | 0.03 | 0.06 | 0.04 | 0.03 | 0.05 | 0.01 | 0.03 | 0.01 | 0.11 | 0.01 | 0.04 | 0.03 | 0.00 | 0.00 | 0.01 | 0.01 | 0.01 | 0.00 | 0.01 | 0.04 | 0.05 | 0.01 | 0.28 | 0.03 | 0.02 | 0.02 | 0.00 | 0.01 | 0.02 | 0.05 | 0.03 | 0.31 | 0.03 | 0.03 | 0.02 | 0.08 | 0.05 | 0.18 | 0.02 | 0.04 | 0.15 | 0.01 | 0.00 | 0.05 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 | 0.00 | 0.03 | 0.05 | 0.00 |
| LYPD5 | ENSG00000159871 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.02 | 0.00 | 0.04 | 0.14 | 0.03 | 0.00 | 0.00 | 0.08 | 0.07 | 0.11 | 0.05 | 0.12 | 0.08 | 0.03 | 0.02 | 0.09 | 0.05 | 0.11 | 0.02 | 0.02 | 0.02 | 0.01 | 0.02 | 0.09 | 0.02 | 0.04 | 0.03 | 0.12 | 0.01 | 0.17 | 0.03 | 0.00 | 0.03 | 0.00 | 0.00 | 0.06 | 0.05 | 0.19 | 0.29 | 0.17 | 0.04 | 0.05 | 0.04 | 0.09 | 0.17 | 0.10 | 0.14 | 0.00 | 0.04 | 0.01 | 0.00 | 0.07 | 0.06 | 0.01 | 0.12 | 0.02 | 0.09 | 0.00 | 0.00 | 0.02 | 0.03 |
| TNFRSF13C | ENSG00000159958 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 | 0.08 | 0.00 | 0.03 | 0.00 | 0.04 | 0.03 | 0.03 | 0.06 | 0.02 | 0.02 | 0.01 | 0.03 | 0.00 | 0.02 | 0.03 | 0.01 | 0.02 | 0.01 | 0.05 | 0.03 | 0.04 | 0.03 | 0.01 | 0.04 | 0.01 | 0.02 | 0.00 | 0.00 | 0.06 | 0.00 | 0.00 | 0.03 | 0.04 | 0.02 | 0.31 | 0.03 | 0.05 | 0.01 | 0.07 | 0.08 | 0.23 | 0.06 | 0.07 | 0.00 | 0.03 | 0.00 | 0.00 | 0.02 | 0.09 | 0.00 | 0.03 | 0.01 | 0.06 | 0.00 | 0.00 | 0.24 | 0.01 |
| OR3A3 | ENSG00000159961 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.06 | 0.04 | 0.03 | 0.00 | 0.00 | 0.01 | 0.02 | 0.01 | 0.06 | 0.02 | 0.02 | 0.01 | 0.03 | 0.04 | 0.04 | 0.01 | 0.02 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 | 0.12 | 0.00 | 0.08 | 0.02 | 0.03 | 0.00 | 0.03 | 0.00 | 0.00 | 0.03 | 0.05 | 0.13 | 0.10 | 0.01 | 0.03 | 0.03 | 0.04 | 0.06 | 0.13 | 0.15 | 0.23 | 0.00 | 0.02 | 0.00 | 0.03 | 0.00 | 0.06 | 0.00 | 0.00 | 0.00 | 0.05 | 0.00 | 0.00 | 0.02 | 0.03 |
| PTGIR | ENSG00000160013 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.04 | 0.07 | 0.03 | 0.00 | 0.02 | 0.00 | 0.08 | 0.04 | 0.07 | 0.06 | 0.10 | 0.02 | 0.02 | 0.05 | 0.04 | 0.08 | 0.03 | 0.01 | 0.02 | 0.01 | 0.02 | 0.02 | 0.04 | 0.03 | 0.04 | 0.12 | 0.06 | 0.14 | 0.03 | 0.00 | 0.02 | 0.00 | 0.00 | 0.05 | 0.07 | 0.06 | 0.33 | 0.05 | 0.06 | 0.03 | 0.05 | 0.11 | 0.19 | 0.04 | 0.18 | 0.00 | 0.04 | 0.01 | 0.00 | 0.26 | 0.03 | 0.00 | 0.13 | 0.01 | 0.13 | 0.00 | 0.00 | 0.02 | 0.03 |
| CALM3 | ENSG00000160014 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.04 | 0.07 | 0.04 | 0.00 | 0.02 | 0.00 | 0.08 | 0.04 | 0.07 | 0.06 | 0.10 | 0.02 | 0.02 | 0.05 | 0.04 | 0.08 | 0.03 | 0.01 | 0.02 | 0.01 | 0.02 | 0.02 | 0.04 | 0.03 | 0.05 | 0.12 | 0.06 | 0.14 | 0.03 | 0.00 | 0.02 | 0.00 | 0.00 | 0.05 | 0.07 | 0.07 | 0.33 | 0.05 | 0.07 | 0.03 | 0.05 | 0.11 | 0.19 | 0.04 | 0.18 | 0.00 | 0.04 | 0.01 | 0.00 | 0.26 | 0.03 | 0.00 | 0.13 | 0.01 | 0.13 | 0.00 | 0.00 | 0.02 | 0.03 |
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