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 |
| NOD2 | ENSG00000167207 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.07 | 0.03 | 0.03 | 0.00 | 0.00 | 0.00 | 0.04 | 0.07 | 0.04 | 0.06 | 0.04 | 0.03 | 0.04 | 0.08 | 0.01 | 0.02 | 0.04 | 0.04 | 0.01 | 0.01 | 0.00 | 0.01 | 0.00 | 0.02 | 0.01 | 0.00 | 0.04 | 0.10 | 0.04 | 0.00 | 0.03 | 0.00 | 0.00 | 0.06 | 0.06 | 0.06 | 0.14 | 0.00 | 0.07 | 0.02 | 0.05 | 0.05 | 0.14 | 0.02 | 0.13 | 0.08 | 0.01 | 0.02 | 0.00 | 0.00 | 0.06 | 0.00 | 0.00 | 0.00 | 0.04 | 0.00 | 0.03 | 0.01 | 0.06 |
| NTN4 | ENSG00000074527 | 0.01 | 0.01 | 0.01 | 0.00 | 0.06 | 0.02 | 0.05 | 0.01 | 0.09 | 0.05 | 0.00 | 0.00 | 0.02 | 0.03 | 0.02 | 0.05 | 0.03 | 0.03 | 0.01 | 0.03 | 0.04 | 0.06 | 0.05 | 0.03 | 0.00 | 0.02 | 0.01 | 0.04 | 0.00 | 0.06 | 0.03 | 0.03 | 0.00 | 0.17 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.07 | 0.06 | 0.07 | 0.21 | 0.02 | 0.02 | 0.03 | 0.03 | 0.17 | 0.11 | 0.39 | 0.04 | 0.00 | 0.01 | 0.00 | 0.01 | 0.08 | 0.02 | 0.00 | 0.02 | 0.00 | 0.02 | 0.02 | 0.00 | 0.03 | 0.08 |
| PDIA6 | ENSG00000143870 | 0.00 | 0.00 | 0.01 | 0.02 | 0.00 | 0.06 | 0.02 | 0.01 | 0.11 | 0.02 | 0.00 | 0.00 | 0.03 | 0.03 | 0.05 | 0.02 | 0.09 | 0.05 | 0.02 | 0.04 | 0.05 | 0.06 | 0.04 | 0.04 | 0.01 | 0.01 | 0.02 | 0.05 | 0.01 | 0.03 | 0.13 | 0.01 | 0.00 | 0.05 | 0.01 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.07 | 0.06 | 0.24 | 0.17 | 0.08 | 0.01 | 0.09 | 0.03 | 0.28 | 0.07 | 0.05 | 0.11 | 0.16 | 0.01 | 0.00 | 0.00 | 0.03 | 0.08 | 0.01 | 0.01 | 0.04 | 0.02 | 0.05 | 0.00 | 0.01 | 0.04 |
| ALDH9A1 | ENSG00000143149 | 0.03 | 0.00 | 0.01 | 0.01 | 0.00 | 0.03 | 0.01 | 0.06 | 0.62 | 0.01 | 0.02 | 0.00 | 0.10 | 0.02 | 0.19 | 0.00 | 0.26 | 0.01 | 0.05 | 0.01 | 0.21 | 0.00 | 0.14 | 0.00 | 0.03 | 0.00 | 0.08 | 0.00 | 0.06 | 0.00 | 0.27 | 0.00 | 0.30 | 0.01 | 0.05 | 0.04 | 0.04 | 0.00 | 0.00 | 0.00 | 0.24 | 0.01 | 0.36 | 0.02 | 0.16 | 0.00 | 0.13 | 0.01 | 0.31 | 0.00 | 0.32 | 0.03 | 0.09 | 0.00 | 0.00 | 0.00 | 0.25 | 0.00 | 0.01 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.14 | 0.01 |
| SERPINB1 | ENSG00000021355 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.05 | 0.18 | 0.11 | 0.00 | 0.05 | 0.02 | 0.01 | 0.09 | 0.02 | 0.10 | 0.09 | 0.05 | 0.06 | 0.11 | 0.24 | 0.05 | 0.10 | 0.02 | 0.03 | 0.02 | 0.04 | 0.00 | 0.07 | 0.18 | 0.02 | 0.06 | 0.08 | 0.04 | 0.05 | 0.00 | 0.01 | 0.00 | 0.00 | 0.10 | 0.08 | 0.43 | 0.11 | 0.10 | 0.06 | 0.08 | 0.02 | 0.21 | 0.05 | 0.06 | 0.13 | 0.04 | 0.03 | 0.00 | 0.00 | 0.14 | 0.01 | 0.02 | 0.04 | 0.02 | 0.03 | 0.22 | 0.00 | 0.22 | 0.01 |
| KSR1 | ENSG00000141068 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.22 | 0.02 | 0.03 | 0.01 | 0.01 | 0.01 | 0.09 | 0.01 | 0.15 | 0.02 | 0.05 | 0.03 | 0.18 | 0.05 | 0.14 | 0.02 | 0.12 | 0.01 | 0.09 | 0.01 | 0.03 | 0.01 | 0.04 | 0.00 | 0.07 | 0.01 | 0.02 | 0.05 | 0.00 | 0.13 | 0.00 | 0.00 | 0.26 | 0.04 | 0.10 | 0.08 | 0.01 | 0.03 | 0.08 | 0.03 | 0.12 | 0.06 | 0.08 | 0.12 | 0.00 | 0.03 | 0.00 | 0.03 | 0.06 | 0.00 | 0.00 | 0.01 | 0.01 | 0.02 | 0.00 | 0.00 | 0.03 | 0.03 |
| SLC17A5 | ENSG00000119899 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.16 | 0.04 | 0.06 | 0.00 | 0.00 | 0.05 | 0.05 | 0.04 | 0.05 | 0.10 | 0.04 | 0.03 | 0.04 | 0.10 | 0.08 | 0.07 | 0.06 | 0.00 | 0.02 | 0.01 | 0.02 | 0.02 | 0.02 | 0.04 | 0.04 | 0.00 | 0.22 | 0.03 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.07 | 0.07 | 0.13 | 0.10 | 0.02 | 0.01 | 0.05 | 0.01 | 0.09 | 0.08 | 0.02 | 0.14 | 0.03 | 0.00 | 0.00 | 0.00 | 0.01 | 0.09 | 0.00 | 0.01 | 0.00 | 0.04 | 0.06 | 0.05 | 0.04 | 0.05 |
| MICAL3 | ENSG00000243156 | 0.01 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.05 | 0.16 | 0.06 | 0.03 | 0.00 | 0.08 | 0.05 | 0.06 | 0.04 | 0.17 | 0.08 | 0.09 | 0.04 | 0.08 | 0.09 | 0.05 | 0.04 | 0.02 | 0.01 | 0.06 | 0.03 | 0.00 | 0.02 | 0.02 | 0.05 | 0.08 | 0.10 | 0.08 | 0.10 | 0.01 | 0.01 | 0.02 | 0.00 | 0.05 | 0.05 | 0.18 | 0.10 | 0.04 | 0.01 | 0.06 | 0.05 | 0.42 | 0.09 | 0.14 | 0.08 | 0.11 | 0.01 | 0.01 | 0.00 | 0.00 | 0.03 | 0.01 | 0.01 | 0.01 | 0.03 | 0.00 | 0.00 | 0.14 | 0.02 |
| IL2RB | ENSG00000100385 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.03 | 0.01 | 0.00 | 0.11 | 0.05 | 0.00 | 0.04 | 0.00 | 0.03 | 0.06 | 0.04 | 0.07 | 0.02 | 0.01 | 0.01 | 0.03 | 0.02 | 0.01 | 0.02 | 0.01 | 0.01 | 0.02 | 0.01 | 0.03 | 0.01 | 0.06 | 0.01 | 0.00 | 0.01 | 0.02 | 0.02 | 0.00 | 0.04 | 0.00 | 0.00 | 0.03 | 0.02 | 0.10 | 0.12 | 0.03 | 0.01 | 0.05 | 0.02 | 0.32 | 0.06 | 0.04 | 0.02 | 0.03 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.03 | 0.00 | 0.00 | 0.14 | 0.02 |
| FXR1 | ENSG00000114416 | 0.06 | 0.00 | 0.03 | 0.00 | 0.00 | 0.01 | 0.05 | 0.02 | 0.17 | 0.01 | 0.00 | 0.00 | 0.00 | 0.08 | 0.15 | 0.04 | 1.92 | 0.00 | 0.71 | 0.00 | 0.79 | 0.03 | 0.24 | 0.01 | 0.04 | 0.01 | 0.08 | 0.02 | 0.03 | 0.00 | 0.11 | 0.02 | 0.12 | 0.01 | 0.10 | 0.03 | 0.00 | 0.10 | 0.00 | 0.00 | 0.24 | 0.01 | 1.14 | 0.03 | 0.69 | 0.00 | 0.37 | 0.01 | 0.81 | 0.07 | 0.12 | 0.09 | 0.20 | 0.00 | 0.00 | 0.00 | 0.06 | 0.00 | 0.07 | 0.00 | 0.21 | 0.01 | 0.00 | 0.00 | 0.02 | 0.04 |
| NRBP2 | ENSG00000185189 | 0.02 | 0.00 | 0.02 | 0.01 | 0.06 | 0.00 | 0.05 | 0.03 | 0.19 | 0.03 | 0.02 | 0.00 | 0.10 | 0.04 | 0.25 | 0.01 | 0.36 | 0.02 | 0.28 | 0.01 | 0.41 | 0.03 | 0.20 | 0.02 | 0.15 | 0.03 | 0.24 | 0.03 | 0.13 | 0.01 | 0.35 | 0.01 | 0.25 | 0.01 | 0.08 | 0.00 | 0.01 | 0.02 | 0.00 | 0.01 | 0.41 | 0.04 | 1.51 | 0.04 | 0.21 | 0.01 | 0.13 | 0.02 | 0.24 | 0.03 | 0.19 | 0.08 | 0.06 | 0.03 | 0.02 | 0.00 | 0.26 | 0.01 | 0.17 | 0.05 | 0.03 | 0.03 | 0.50 | 0.00 | 0.24 | 0.02 |
| EMID1 | ENSG00000186998 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.05 | 0.22 | 0.01 | 0.00 | 0.07 | 0.00 | 0.00 | 0.03 | 0.03 | 0.15 | 0.01 | 0.04 | 0.01 | 0.04 | 0.01 | 0.03 | 0.02 | 0.03 | 0.01 | 0.04 | 0.01 | 0.01 | 0.03 | 0.02 | 0.03 | 0.00 | 0.11 | 0.01 | 0.10 | 0.00 | 0.01 | 0.00 | 0.00 | 0.05 | 0.03 | 0.18 | 0.08 | 0.04 | 0.00 | 0.08 | 0.02 | 0.35 | 0.03 | 0.03 | 0.05 | 0.10 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.03 | 0.00 | 0.00 | 0.03 | 0.06 |
| IKBKG | ENSG00000269335 | 0.03 | 0.02 | 0.02 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.12 | 0.04 | 0.06 | 0.00 | 0.06 | 0.03 | 0.23 | 0.02 | 0.19 | 0.04 | 0.14 | 0.01 | 0.21 | 0.02 | 0.17 | 0.04 | 0.05 | 0.01 | 0.11 | 0.01 | 0.06 | 0.01 | 0.13 | 0.03 | 0.10 | 0.02 | 0.13 | 0.02 | 0.00 | 0.01 | 0.00 | 0.01 | 0.10 | 0.03 | 0.45 | 0.13 | 0.23 | 0.02 | 0.11 | 0.04 | 0.09 | 0.10 | 0.24 | 0.13 | 0.01 | 0.03 | 0.00 | 0.00 | 0.15 | 0.07 | 0.02 | 0.03 | 0.04 | 0.03 | 0.05 | 0.00 | 0.07 | 0.01 |
| GDF5 | ENSG00000125965 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.02 | 0.02 | 0.12 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.11 | 0.01 | 0.16 | 0.01 | 0.11 | 0.00 | 0.08 | 0.01 | 0.06 | 0.00 | 0.10 | 0.00 | 0.17 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.06 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.16 | 0.02 | 0.16 | 0.04 | 0.12 | 0.00 | 0.07 | 0.01 | 0.13 | 0.00 | 0.12 | 0.03 | 0.00 | 0.01 | 0.00 | 0.03 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.01 |
| SERPINI1 | ENSG00000163536 | 0.05 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.08 | 0.01 | 0.16 | 0.01 | 0.00 | 0.00 | 0.00 | 0.03 | 0.18 | 0.01 | 1.58 | 0.00 | 0.57 | 0.00 | 0.80 | 0.00 | 0.23 | 0.00 | 0.03 | 0.01 | 0.04 | 0.01 | 0.04 | 0.00 | 0.12 | 0.01 | 0.08 | 0.01 | 0.10 | 0.00 | 0.00 | 0.06 | 0.00 | 0.00 | 0.19 | 0.01 | 1.27 | 0.02 | 0.68 | 0.00 | 0.28 | 0.01 | 0.61 | 0.00 | 0.05 | 0.11 | 0.20 | 0.00 | 0.00 | 0.00 | 0.05 | 0.00 | 0.03 | 0.01 | 0.05 | 0.02 | 0.00 | 0.00 | 0.02 | 0.03 |
| G2E3 | ENSG00000092140 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.05 | 0.06 | 0.00 | 0.00 | 0.00 | 0.02 | 0.37 | 0.02 | 0.09 | 0.05 | 0.05 | 0.05 | 0.13 | 0.04 | 0.07 | 0.03 | 0.03 | 0.02 | 0.01 | 0.06 | 0.00 | 0.01 | 0.06 | 0.02 | 0.05 | 0.02 | 0.10 | 0.05 | 0.00 | 0.01 | 0.00 | 0.00 | 0.14 | 0.03 | 0.20 | 0.11 | 0.04 | 0.01 | 0.05 | 0.03 | 0.04 | 0.07 | 0.19 | 0.04 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 | 0.01 | 0.09 | 0.00 | 0.00 | 0.02 | 0.02 |
| COL15A1 | ENSG00000204291 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.02 | 0.08 | 0.00 | 0.01 | 0.02 | 0.06 | 0.01 | 0.04 | 0.04 | 0.01 | 0.04 | 0.00 | 0.09 | 0.01 | 0.03 | 0.04 | 0.01 | 0.01 | 0.04 | 0.03 | 0.00 | 0.04 | 0.01 | 0.05 | 0.00 | 0.08 | 0.11 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.03 | 0.05 | 0.06 | 0.14 | 0.02 | 0.02 | 0.01 | 0.04 | 0.00 | 0.15 | 0.11 | 0.03 | 0.04 | 0.02 | 0.00 | 0.02 | 0.00 | 0.03 | 0.01 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.02 |
| FOS | ENSG00000170345 | 0.01 | 0.03 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.05 | 0.05 | 0.04 | 0.00 | 0.01 | 0.00 | 0.06 | 0.04 | 0.05 | 0.06 | 0.03 | 0.05 | 0.01 | 0.13 | 0.02 | 0.08 | 0.04 | 0.00 | 0.03 | 0.01 | 0.03 | 0.03 | 0.01 | 0.03 | 0.10 | 0.00 | 0.26 | 0.04 | 0.03 | 0.01 | 0.04 | 0.00 | 0.00 | 0.02 | 0.10 | 0.13 | 0.18 | 0.06 | 0.03 | 0.04 | 0.02 | 0.04 | 0.06 | 0.07 | 0.11 | 0.03 | 0.01 | 0.00 | 0.00 | 0.04 | 0.00 | 0.00 | 0.12 | 0.02 | 0.08 | 0.03 | 0.00 | 0.00 | 0.05 |
| CYP2A6 | ENSG00000255974 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.02 | 0.01 | 0.04 | 0.17 | 0.02 | 0.00 | 0.00 | 0.08 | 0.02 | 0.11 | 0.03 | 0.29 | 0.07 | 0.03 | 0.02 | 0.05 | 0.05 | 0.07 | 0.02 | 0.04 | 0.01 | 0.01 | 0.01 | 0.11 | 0.02 | 0.09 | 0.02 | 0.12 | 0.01 | 0.05 | 0.04 | 0.00 | 0.02 | 0.00 | 0.00 | 0.08 | 0.04 | 0.31 | 0.25 | 0.10 | 0.04 | 0.09 | 0.04 | 0.33 | 0.14 | 0.23 | 0.12 | 0.00 | 0.03 | 0.01 | 0.00 | 0.05 | 0.00 | 0.02 | 0.07 | 0.02 | 0.08 | 0.00 | 0.00 | 0.02 | 0.02 |
| ATP8A2 | ENSG00000132932 | 0.01 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.03 | 0.11 | 0.05 | 0.00 | 0.02 | 0.00 | 0.18 | 0.01 | 0.11 | 0.03 | 0.12 | 0.03 | 0.13 | 0.08 | 0.10 | 0.08 | 0.04 | 0.24 | 0.01 | 0.23 | 0.02 | 0.02 | 0.00 | 0.03 | 0.11 | 0.00 | 0.15 | 0.00 | 0.09 | 0.00 | 0.00 | 0.00 | 0.01 | 0.09 | 0.07 | 0.08 | 0.19 | 0.03 | 0.13 | 0.02 | 0.05 | 0.01 | 0.16 | 0.13 | 0.19 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.05 | 0.01 | 0.06 | 0.01 | 0.06 | 0.00 | 0.00 | 0.05 | 0.03 |
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