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 |
| MME | ENSG00000196549 | 0.03 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.05 | 0.02 | 0.11 | 0.01 | 0.00 | 0.00 | 0.00 | 0.03 | 0.12 | 0.01 | 0.90 | 0.00 | 0.47 | 0.00 | 0.60 | 0.01 | 0.14 | 0.01 | 0.02 | 0.00 | 0.05 | 0.01 | 0.03 | 0.00 | 0.08 | 0.02 | 0.03 | 0.03 | 0.10 | 0.01 | 0.00 | 0.06 | 0.00 | 0.00 | 0.15 | 0.01 | 0.69 | 0.02 | 0.45 | 0.01 | 0.16 | 0.01 | 0.26 | 0.02 | 0.05 | 0.07 | 0.12 | 0.00 | 0.00 | 0.00 | 0.01 | 0.05 | 0.01 | 0.01 | 0.02 | 0.03 | 0.00 | 0.00 | 0.01 | 0.03 |
| NCOR2 | ENSG00000196498 | 0.01 | 0.01 | 0.02 | 0.00 | 0.07 | 0.02 | 0.03 | 0.08 | 0.09 | 0.04 | 0.00 | 0.00 | 0.01 | 0.02 | 0.04 | 0.05 | 0.03 | 0.07 | 0.03 | 0.05 | 0.11 | 0.07 | 0.07 | 0.05 | 0.01 | 0.01 | 0.05 | 0.01 | 0.00 | 0.05 | 0.03 | 0.12 | 0.00 | 0.17 | 0.08 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.06 | 0.10 | 0.17 | 0.24 | 0.03 | 0.01 | 0.05 | 0.07 | 0.09 | 0.16 | 0.13 | 0.06 | 0.01 | 0.00 | 0.01 | 0.01 | 0.07 | 0.03 | 0.03 | 0.01 | 0.03 | 0.01 | 0.00 | 0.00 | 0.04 | 0.08 |
| COL2A1 | ENSG00000139219 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.08 | 0.03 | 0.00 | 0.00 | 0.00 | 0.04 | 0.05 | 0.02 | 0.07 | 0.02 | 0.02 | 0.03 | 0.05 | 0.04 | 0.07 | 0.03 | 0.02 | 0.01 | 0.03 | 0.01 | 0.00 | 0.04 | 0.02 | 0.01 | 0.00 | 0.01 | 0.23 | 0.01 | 0.01 | 0.03 | 0.00 | 0.00 | 0.04 | 0.05 | 0.14 | 0.06 | 0.03 | 0.00 | 0.11 | 0.02 | 0.29 | 0.13 | 0.16 | 0.08 | 0.02 | 0.00 | 0.00 | 0.01 | 0.13 | 0.03 | 0.01 | 0.04 | 0.01 | 0.05 | 0.00 | 0.00 | 0.08 | 0.04 |
| DIDO1 | ENSG00000101191 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.04 | 0.00 | 0.06 | 0.04 | 0.00 | 0.00 | 0.03 | 0.00 | 0.28 | 0.01 | 0.07 | 0.04 | 0.02 | 0.01 | 0.15 | 0.01 | 0.17 | 0.01 | 0.09 | 0.00 | 0.12 | 0.01 | 0.03 | 0.00 | 0.11 | 0.00 | 0.00 | 0.01 | 0.05 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.34 | 0.02 | 0.48 | 0.04 | 0.05 | 0.03 | 0.12 | 0.01 | 0.17 | 0.00 | 0.19 | 0.06 | 0.02 | 0.02 | 0.03 | 0.00 | 0.04 | 0.00 | 0.02 | 0.00 | 0.01 | 0.02 | 0.00 | 0.00 | 0.12 | 0.00 |
| OLFML1 | ENSG00000183801 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 | 0.02 | 0.00 | 0.10 | 0.00 | 0.00 | 0.02 | 0.07 | 0.01 | 0.06 | 0.01 | 0.13 | 0.01 | 0.06 | 0.04 | 0.08 | 0.02 | 0.04 | 0.01 | 0.01 | 0.01 | 0.02 | 0.00 | 0.05 | 0.03 | 0.02 | 0.03 | 0.01 | 0.01 | 0.04 | 0.03 | 0.07 | 0.00 | 0.00 | 0.04 | 0.09 | 0.01 | 0.40 | 0.01 | 0.05 | 0.02 | 0.07 | 0.06 | 0.05 | 0.08 | 0.12 | 0.02 | 0.00 | 0.00 | 0.00 | 0.05 | 0.00 | 0.01 | 0.08 | 0.00 | 0.04 | 0.00 | 0.00 | 0.02 | 0.02 |
| PHIP | ENSG00000146247 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.20 | 0.03 | 0.08 | 0.00 | 0.00 | 0.01 | 0.03 | 0.03 | 0.04 | 0.10 | 0.03 | 0.03 | 0.04 | 0.03 | 0.07 | 0.04 | 0.07 | 0.00 | 0.02 | 0.01 | 0.01 | 0.00 | 0.02 | 0.03 | 0.05 | 0.00 | 0.21 | 0.06 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.07 | 0.08 | 0.15 | 0.11 | 0.03 | 0.01 | 0.02 | 0.01 | 0.08 | 0.06 | 0.07 | 0.14 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.29 | 0.00 | 0.00 | 0.00 | 0.04 | 0.04 | 0.03 | 0.02 | 0.04 |
| OPRL1 | ENSG00000125510 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.05 | 0.01 | 0.08 | 0.04 | 0.00 | 0.00 | 0.03 | 0.00 | 0.32 | 0.01 | 0.08 | 0.04 | 0.03 | 0.01 | 0.17 | 0.01 | 0.16 | 0.00 | 0.09 | 0.00 | 0.13 | 0.01 | 0.02 | 0.00 | 0.11 | 0.00 | 0.00 | 0.01 | 0.05 | 0.02 | 0.00 | 0.03 | 0.00 | 0.00 | 0.36 | 0.02 | 0.52 | 0.04 | 0.04 | 0.02 | 0.15 | 0.01 | 0.44 | 0.00 | 0.20 | 0.11 | 0.03 | 0.03 | 0.03 | 0.00 | 0.04 | 0.00 | 0.02 | 0.02 | 0.02 | 0.02 | 0.00 | 0.00 | 0.15 | 0.00 |
| ATP2C2 | ENSG00000064270 | 0.00 | 0.00 | 0.00 | 0.04 | 0.00 | 0.08 | 0.00 | 0.28 | 0.07 | 0.05 | 0.00 | 0.00 | 0.00 | 0.17 | 0.01 | 0.09 | 0.03 | 0.08 | 0.03 | 0.04 | 0.06 | 0.04 | 0.03 | 0.04 | 0.01 | 0.03 | 0.02 | 0.04 | 0.02 | 0.02 | 0.00 | 0.06 | 0.05 | 0.01 | 0.06 | 0.05 | 0.00 | 0.01 | 0.00 | 0.01 | 0.04 | 0.08 | 0.05 | 0.33 | 0.03 | 0.04 | 0.01 | 0.08 | 0.01 | 0.27 | 0.06 | 0.07 | 0.00 | 0.10 | 0.00 | 0.05 | 0.03 | 0.00 | 0.00 | 0.01 | 0.01 | 0.04 | 0.00 | 0.00 | 0.01 | 0.09 |
| TF | ENSG00000091513 | 0.02 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.06 | 0.01 | 0.05 | 0.02 | 0.00 | 0.01 | 0.00 | 0.01 | 0.04 | 0.01 | 0.19 | 0.01 | 0.14 | 0.00 | 0.17 | 0.02 | 0.07 | 0.02 | 0.01 | 0.01 | 0.02 | 0.01 | 0.01 | 0.00 | 0.07 | 0.02 | 0.00 | 0.05 | 0.06 | 0.02 | 0.00 | 0.06 | 0.00 | 0.00 | 0.06 | 0.03 | 0.34 | 0.03 | 0.17 | 0.01 | 0.07 | 0.00 | 0.19 | 0.02 | 0.02 | 0.05 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.02 | 0.01 | 0.02 | 0.01 | 0.05 | 0.00 | 0.00 | 0.00 | 0.04 |
| PDE6B | ENSG00000133256 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.04 | 0.02 | 0.10 | 0.05 | 0.02 | 0.02 | 0.01 | 0.03 | 0.06 | 0.05 | 0.05 | 0.07 | 0.03 | 0.07 | 0.11 | 0.09 | 0.09 | 0.05 | 0.02 | 0.03 | 0.05 | 0.04 | 0.10 | 0.02 | 0.04 | 0.07 | 0.00 | 0.01 | 0.22 | 0.03 | 0.00 | 0.00 | 0.01 | 0.00 | 0.04 | 0.08 | 0.42 | 0.11 | 0.02 | 0.06 | 0.08 | 0.06 | 0.15 | 0.03 | 0.14 | 0.07 | 0.02 | 0.02 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.02 | 0.01 | 0.04 | 0.02 | 0.00 | 0.04 | 0.05 |
| TLR4 | ENSG00000136869 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.04 | 0.01 | 0.02 | 0.03 | 0.00 | 0.00 | 0.01 | 0.00 | 0.05 | 0.02 | 0.06 | 0.01 | 0.05 | 0.01 | 0.09 | 0.02 | 0.06 | 0.02 | 0.01 | 0.01 | 0.04 | 0.02 | 0.00 | 0.01 | 0.03 | 0.04 | 0.06 | 0.04 | 0.09 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.06 | 0.04 | 0.09 | 0.11 | 0.04 | 0.00 | 0.01 | 0.04 | 0.00 | 0.15 | 0.05 | 0.03 | 0.03 | 0.02 | 0.00 | 0.00 | 0.05 | 0.00 | 0.00 | 0.01 | 0.02 | 0.01 | 0.00 | 0.00 | 0.02 | 0.02 |
| SMARCC1 | ENSG00000173473 | 0.00 | 0.18 | 0.00 | 0.02 | 0.05 | 0.00 | 0.01 | 0.04 | 0.03 | 0.13 | 0.00 | 0.04 | 0.00 | 0.55 | 0.01 | 0.07 | 0.00 | 0.09 | 0.01 | 0.05 | 0.02 | 0.08 | 0.00 | 0.11 | 0.00 | 0.05 | 0.02 | 0.07 | 0.01 | 0.05 | 0.03 | 0.05 | 0.00 | 0.24 | 0.04 | 0.02 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.16 | 0.09 | 0.20 | 0.01 | 0.06 | 0.05 | 0.05 | 0.06 | 0.28 | 0.04 | 0.13 | 0.01 | 0.04 | 0.00 | 0.01 | 0.00 | 0.14 | 0.00 | 0.06 | 0.01 | 0.04 | 0.00 | 0.03 | 0.01 | 0.05 |
| TAB2 | ENSG00000055208 | 0.00 | 0.06 | 0.00 | 0.01 | 0.00 | 0.05 | 0.01 | 0.03 | 0.04 | 0.08 | 0.00 | 0.03 | 0.00 | 0.19 | 0.01 | 0.06 | 0.05 | 0.05 | 0.03 | 0.03 | 0.10 | 0.04 | 0.09 | 0.05 | 0.02 | 0.01 | 0.04 | 0.04 | 0.00 | 0.03 | 0.01 | 0.12 | 0.00 | 0.16 | 0.10 | 0.03 | 0.00 | 0.02 | 0.00 | 0.00 | 0.10 | 0.08 | 0.03 | 0.41 | 0.01 | 0.09 | 0.03 | 0.04 | 0.08 | 0.03 | 0.52 | 0.02 | 0.01 | 0.04 | 0.00 | 0.00 | 0.00 | 0.09 | 0.00 | 0.05 | 0.01 | 0.10 | 0.05 | 0.09 | 0.01 | 0.13 |
| TGFBI | ENSG00000120708 | 0.28 | 0.01 | 0.02 | 0.01 | 0.00 | 0.00 | 0.03 | 0.03 | 0.05 | 0.05 | 0.00 | 0.00 | 0.00 | 0.04 | 0.00 | 0.07 | 0.01 | 0.04 | 0.01 | 0.04 | 0.03 | 0.05 | 0.02 | 0.08 | 0.01 | 0.04 | 0.02 | 0.03 | 0.01 | 0.03 | 0.06 | 0.04 | 0.09 | 0.01 | 0.24 | 0.04 | 0.00 | 0.06 | 0.01 | 0.00 | 0.02 | 0.03 | 0.11 | 0.14 | 0.03 | 0.02 | 0.01 | 0.01 | 0.10 | 0.01 | 0.08 | 0.04 | 0.00 | 0.00 | 0.00 | 0.10 | 0.04 | 0.00 | 0.00 | 0.03 | 0.01 | 0.02 | 0.00 | 0.03 | 0.04 | 0.10 |
| ADAMTS2 | ENSG00000087116 | 0.33 | 0.01 | 0.06 | 0.01 | 0.00 | 0.00 | 0.04 | 0.01 | 0.02 | 0.10 | 0.00 | 0.01 | 0.03 | 0.05 | 0.09 | 0.04 | 0.03 | 0.06 | 0.03 | 0.07 | 0.17 | 0.02 | 0.04 | 0.04 | 0.03 | 0.02 | 0.04 | 0.03 | 0.03 | 0.01 | 0.18 | 0.02 | 0.05 | 0.01 | 0.37 | 0.02 | 0.01 | 0.03 | 0.01 | 0.00 | 0.11 | 0.04 | 0.24 | 0.14 | 0.04 | 0.05 | 0.07 | 0.02 | 0.15 | 0.02 | 0.18 | 0.09 | 0.00 | 0.01 | 0.00 | 0.02 | 0.02 | 0.00 | 0.01 | 0.06 | 0.02 | 0.05 | 0.04 | 0.02 | 0.09 | 0.09 |
| SCG3 | ENSG00000104112 | 0.00 | 0.00 | 0.00 | 0.01 | 0.14 | 0.01 | 0.01 | 0.04 | 0.03 | 0.03 | 0.00 | 0.00 | 0.08 | 0.12 | 0.01 | 0.04 | 0.04 | 0.05 | 0.04 | 0.03 | 0.03 | 0.02 | 0.02 | 0.06 | 0.01 | 0.03 | 0.00 | 0.05 | 0.00 | 0.02 | 0.01 | 0.02 | 0.00 | 0.01 | 0.02 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.07 | 0.07 | 0.10 | 0.19 | 0.01 | 0.10 | 0.01 | 0.07 | 0.09 | 0.26 | 0.09 | 0.04 | 0.02 | 0.02 | 0.00 | 0.00 | 0.06 | 0.05 | 0.00 | 0.02 | 0.00 | 0.07 | 0.00 | 0.00 | 0.03 | 0.09 |
| RYR1 | ENSG00000196218 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.02 | 0.02 | 0.01 | 0.33 | 0.02 | 0.00 | 0.00 | 0.08 | 0.02 | 0.20 | 0.03 | 0.54 | 0.03 | 0.07 | 0.01 | 0.14 | 0.03 | 0.11 | 0.02 | 0.05 | 0.01 | 0.01 | 0.01 | 0.19 | 0.00 | 0.03 | 0.01 | 0.12 | 0.03 | 0.06 | 0.03 | 0.01 | 0.02 | 0.00 | 0.00 | 0.15 | 0.03 | 0.73 | 0.12 | 0.30 | 0.03 | 0.18 | 0.03 | 1.27 | 0.09 | 0.28 | 0.10 | 0.00 | 0.03 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.04 | 0.05 | 0.03 | 0.00 | 0.00 | 0.04 | 0.01 |
| COL16A1 | ENSG00000084636 | 0.00 | 0.04 | 0.00 | 0.05 | 0.00 | 0.00 | 0.03 | 0.02 | 0.04 | 0.07 | 0.00 | 0.01 | 0.11 | 0.07 | 0.05 | 0.04 | 0.05 | 0.06 | 0.04 | 0.05 | 0.09 | 0.09 | 0.04 | 0.07 | 0.02 | 0.10 | 0.01 | 0.13 | 0.02 | 0.03 | 0.00 | 0.19 | 0.00 | 0.73 | 0.00 | 0.03 | 0.02 | 0.08 | 0.00 | 0.00 | 0.07 | 0.10 | 0.24 | 0.26 | 0.05 | 0.03 | 0.10 | 0.08 | 0.19 | 0.06 | 0.13 | 0.06 | 0.03 | 0.03 | 0.02 | 0.00 | 0.00 | 0.07 | 0.00 | 0.01 | 0.03 | 0.04 | 0.00 | 0.07 | 0.06 | 0.06 |
| ADAMTS17 | ENSG00000140470 | 0.00 | 0.00 | 0.01 | 0.00 | 0.02 | 0.00 | 0.02 | 0.02 | 0.05 | 0.02 | 0.03 | 0.02 | 0.06 | 0.00 | 0.07 | 0.02 | 0.27 | 0.01 | 0.12 | 0.01 | 0.25 | 0.02 | 0.24 | 0.01 | 0.04 | 0.01 | 0.08 | 0.02 | 0.06 | 0.00 | 0.12 | 0.07 | 0.05 | 0.01 | 0.09 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.19 | 0.03 | 0.45 | 0.08 | 0.18 | 0.01 | 0.08 | 0.02 | 0.14 | 0.04 | 0.27 | 0.08 | 0.01 | 0.03 | 0.00 | 0.00 | 0.06 | 0.00 | 0.02 | 0.01 | 0.02 | 0.02 | 0.00 | 0.00 | 0.19 | 0.02 |
| PDIA4 | ENSG00000155660 | 0.03 | 0.01 | 0.06 | 0.00 | 0.05 | 0.02 | 0.03 | 0.02 | 0.03 | 0.06 | 0.00 | 0.01 | 0.03 | 0.03 | 0.10 | 0.02 | 0.09 | 0.08 | 0.02 | 0.16 | 0.03 | 0.25 | 0.02 | 0.10 | 0.02 | 0.01 | 0.01 | 0.02 | 0.02 | 0.05 | 0.07 | 0.05 | 0.00 | 0.11 | 0.03 | 0.06 | 0.00 | 0.03 | 0.00 | 0.00 | 0.09 | 0.07 | 0.56 | 0.07 | 0.03 | 0.09 | 0.04 | 0.06 | 0.21 | 0.19 | 0.14 | 0.15 | 0.01 | 0.05 | 0.00 | 0.06 | 0.00 | 0.13 | 0.11 | 0.01 | 0.06 | 0.01 | 0.00 | 0.03 | 0.21 | 0.03 |
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