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 |
| KCNJ6 | ENSG00000157542 | 0.00 | 0.00 | 0.01 | 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 | 0.02 | 0.04 | 0.03 | 0.10 | 0.02 | 0.08 | 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 | 0.09 | 0.01 | 0.13 | 0.10 | 0.14 | 0.01 | 0.04 | 0.01 | 0.04 | 0.03 | 0.08 | 0.08 | 0.04 | 0.00 | 0.11 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.02 | 0.03 | 0.00 | 0.01 | 0.01 |
| SLC34A1 | ENSG00000131183 | 0.34 | 0.01 | 0.06 | 0.01 | 0.00 | 0.00 | 0.04 | 0.00 | 0.02 | 0.11 | 0.00 | 0.01 | 0.03 | 0.05 | 0.09 | 0.04 | 0.04 | 0.05 | 0.02 | 0.06 | 0.13 | 0.01 | 0.04 | 0.04 | 0.02 | 0.02 | 0.04 | 0.03 | 0.03 | 0.01 | 0.15 | 0.02 | 0.05 | 0.01 | 0.55 | 0.02 | 0.01 | 0.03 | 0.01 | 0.00 | 0.11 | 0.03 | 0.28 | 0.12 | 0.03 | 0.04 | 0.10 | 0.02 | 0.32 | 0.01 | 0.14 | 0.09 | 0.00 | 0.01 | 0.00 | 0.02 | 0.02 | 0.00 | 0.01 | 0.06 | 0.03 | 0.04 | 0.04 | 0.00 | 0.10 | 0.09 |
| SLC22A8 | ENSG00000149452 | 0.01 | 0.00 | 0.00 | 0.01 | 0.09 | 0.00 | 0.02 | 0.01 | 0.13 | 0.01 | 0.00 | 0.00 | 0.12 | 0.02 | 0.05 | 0.02 | 0.05 | 0.01 | 0.13 | 0.03 | 0.13 | 0.02 | 0.03 | 0.02 | 0.01 | 0.02 | 0.02 | 0.03 | 0.00 | 0.03 | 0.02 | 0.03 | 0.00 | 0.07 | 0.08 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.08 | 0.07 | 0.14 | 0.04 | 0.06 | 0.01 | 0.08 | 0.02 | 0.29 | 0.12 | 0.07 | 0.02 | 0.00 | 0.07 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.04 | 0.05 |
| KCNH1 | ENSG00000143473 | 0.01 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.05 | 0.07 | 0.06 | 0.01 | 0.00 | 0.07 | 0.03 | 0.11 | 0.01 | 0.10 | 0.01 | 0.05 | 0.01 | 0.16 | 0.05 | 0.06 | 0.03 | 0.03 | 0.01 | 0.08 | 0.03 | 0.00 | 0.00 | 0.15 | 0.02 | 0.16 | 0.02 | 0.01 | 0.05 | 0.01 | 0.00 | 0.00 | 0.00 | 0.21 | 0.01 | 0.15 | 0.17 | 0.06 | 0.01 | 0.06 | 0.03 | 0.13 | 0.04 | 0.04 | 0.21 | 0.02 | 0.03 | 0.01 | 0.00 | 0.16 | 0.04 | 0.01 | 0.01 | 0.02 | 0.04 | 0.09 | 0.00 | 0.12 | 0.03 |
| KCNH4 | ENSG00000089558 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.08 | 0.05 | 0.02 | 0.00 | 0.00 | 0.01 | 0.02 | 0.06 | 0.01 | 0.03 | 0.05 | 0.03 | 0.01 | 0.19 | 0.04 | 0.13 | 0.03 | 0.05 | 0.01 | 0.04 | 0.02 | 0.03 | 0.03 | 0.02 | 0.04 | 0.02 | 0.01 | 0.02 | 0.14 | 0.00 | 0.12 | 0.00 | 0.00 | 0.05 | 0.10 | 0.01 | 0.15 | 0.05 | 0.04 | 0.03 | 0.07 | 0.00 | 0.20 | 0.05 | 0.10 | 0.01 | 0.01 | 0.00 | 0.02 | 0.06 | 0.00 | 0.00 | 0.01 | 0.01 | 0.03 | 0.00 | 0.05 | 0.01 | 0.03 |
| ABCC12 | ENSG00000140798 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.06 | 0.01 | 0.08 | 0.02 | 0.01 | 0.00 | 0.00 | 0.04 | 0.08 | 0.04 | 0.05 | 0.03 | 0.05 | 0.03 | 0.10 | 0.02 | 0.03 | 0.03 | 0.04 | 0.01 | 0.02 | 0.01 | 0.01 | 0.00 | 0.03 | 0.01 | 0.00 | 0.08 | 0.08 | 0.04 | 0.00 | 0.02 | 0.00 | 0.00 | 0.11 | 0.05 | 0.10 | 0.12 | 0.01 | 0.07 | 0.03 | 0.05 | 0.02 | 0.14 | 0.04 | 0.12 | 0.08 | 0.01 | 0.02 | 0.00 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.10 | 0.01 | 0.07 |
| SLC6A18 | ENSG00000164363 | 0.01 | 0.01 | 0.03 | 0.01 | 0.07 | 0.11 | 0.03 | 0.01 | 0.28 | 0.02 | 0.00 | 0.01 | 0.06 | 0.00 | 0.41 | 0.01 | 0.38 | 0.01 | 0.16 | 0.01 | 0.33 | 0.03 | 0.18 | 0.02 | 0.04 | 0.02 | 0.06 | 0.02 | 0.03 | 0.01 | 0.27 | 0.02 | 0.00 | 0.05 | 0.77 | 0.03 | 0.01 | 0.00 | 0.00 | 0.01 | 0.13 | 0.02 | 0.48 | 0.05 | 0.21 | 0.02 | 0.16 | 0.01 | 0.26 | 0.03 | 0.42 | 0.13 | 0.03 | 0.03 | 0.00 | 0.00 | 0.17 | 0.00 | 0.03 | 0.06 | 0.06 | 0.04 | 0.03 | 0.02 | 0.35 | 0.07 |
| MUSK | ENSG00000030304 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 | 0.06 | 0.04 | 0.00 | 0.00 | 0.02 | 0.02 | 0.05 | 0.02 | 0.04 | 0.01 | 0.06 | 0.01 | 0.09 | 0.02 | 0.04 | 0.02 | 0.00 | 0.01 | 0.04 | 0.02 | 0.00 | 0.01 | 0.02 | 0.04 | 0.00 | 0.11 | 0.06 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.05 | 0.09 | 0.12 | 0.02 | 0.01 | 0.01 | 0.04 | 0.00 | 0.15 | 0.08 | 0.02 | 0.04 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 | 0.01 | 0.00 | 0.00 | 0.03 | 0.02 |
| BPIFC | ENSG00000184459 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.02 | 0.16 | 0.01 | 0.02 | 0.03 | 0.00 | 0.01 | 0.04 | 0.02 | 0.12 | 0.01 | 0.01 | 0.00 | 0.04 | 0.01 | 0.02 | 0.02 | 0.02 | 0.01 | 0.02 | 0.01 | 0.01 | 0.02 | 0.02 | 0.01 | 0.00 | 0.01 | 0.00 | 0.02 | 0.00 | 0.02 | 0.00 | 0.00 | 0.03 | 0.03 | 0.16 | 0.06 | 0.02 | 0.00 | 0.06 | 0.02 | 0.20 | 0.07 | 0.07 | 0.04 | 0.05 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.00 | 0.04 | 0.00 | 0.00 | 0.05 | 0.04 |
| ADCY10 | ENSG00000143199 | 0.03 | 0.00 | 0.01 | 0.01 | 0.00 | 0.03 | 0.01 | 0.05 | 0.51 | 0.01 | 0.02 | 0.02 | 0.10 | 0.03 | 0.15 | 0.01 | 0.24 | 0.01 | 0.05 | 0.01 | 0.21 | 0.01 | 0.11 | 0.00 | 0.03 | 0.00 | 0.08 | 0.00 | 0.06 | 0.00 | 0.28 | 0.00 | 0.30 | 0.01 | 0.00 | 0.04 | 0.04 | 0.00 | 0.00 | 0.00 | 0.21 | 0.01 | 0.34 | 0.02 | 0.15 | 0.00 | 0.11 | 0.01 | 0.32 | 0.00 | 0.46 | 0.03 | 0.09 | 0.00 | 0.00 | 0.00 | 0.28 | 0.00 | 0.01 | 0.00 | 0.02 | 0.01 | 0.00 | 0.00 | 0.15 | 0.01 |
| GLRA1 | ENSG00000145888 | 0.30 | 0.00 | 0.04 | 0.01 | 0.00 | 0.00 | 0.02 | 0.02 | 0.01 | 0.05 | 0.00 | 0.00 | 0.02 | 0.03 | 0.04 | 0.04 | 0.01 | 0.03 | 0.01 | 0.04 | 0.03 | 0.02 | 0.04 | 0.04 | 0.01 | 0.02 | 0.04 | 0.01 | 0.02 | 0.01 | 0.10 | 0.02 | 0.09 | 0.01 | 0.26 | 0.04 | 0.00 | 0.03 | 0.02 | 0.00 | 0.04 | 0.03 | 0.16 | 0.12 | 0.03 | 0.02 | 0.04 | 0.02 | 0.05 | 0.02 | 0.07 | 0.06 | 0.00 | 0.00 | 0.00 | 0.09 | 0.04 | 0.00 | 0.00 | 0.06 | 0.01 | 0.04 | 0.00 | 0.03 | 0.04 | 0.14 |
| CSN1S1 | ENSG00000126545 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.03 | 0.12 | 0.02 | 0.00 | 0.00 | 0.00 | 0.07 | 0.07 | 0.03 | 0.21 | 0.01 | 0.09 | 0.02 | 0.13 | 0.02 | 0.05 | 0.03 | 0.01 | 0.01 | 0.04 | 0.01 | 0.00 | 0.01 | 0.04 | 0.07 | 0.00 | 0.03 | 0.03 | 0.00 | 0.02 | 0.02 | 0.00 | 0.00 | 0.09 | 0.02 | 0.24 | 0.08 | 0.04 | 0.04 | 0.04 | 0.01 | 0.06 | 0.05 | 0.05 | 0.05 | 0.08 | 0.01 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.03 | 0.00 | 0.02 | 0.00 | 0.00 | 0.02 | 0.03 |
| MMP20 | ENSG00000137674 | 0.02 | 0.00 | 0.00 | 0.05 | 0.03 | 0.03 | 0.02 | 0.05 | 0.28 | 0.05 | 0.00 | 0.00 | 0.06 | 0.06 | 0.11 | 0.04 | 0.11 | 0.07 | 0.43 | 0.09 | 0.14 | 0.08 | 0.10 | 0.05 | 0.04 | 0.01 | 0.02 | 0.02 | 0.03 | 0.01 | 0.05 | 0.06 | 0.00 | 0.10 | 0.01 | 0.05 | 0.00 | 0.04 | 0.00 | 0.00 | 0.07 | 0.18 | 0.37 | 0.12 | 0.76 | 0.10 | 0.11 | 0.04 | 0.22 | 0.17 | 0.30 | 0.12 | 0.01 | 0.08 | 0.02 | 0.00 | 0.04 | 0.01 | 0.01 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.18 | 0.12 |
| SLC2A7 | ENSG00000197241 | 0.00 | 0.06 | 0.01 | 0.08 | 0.00 | 0.00 | 0.01 | 0.06 | 0.09 | 0.08 | 0.00 | 0.02 | 0.04 | 0.27 | 0.06 | 0.06 | 0.06 | 0.11 | 0.05 | 0.08 | 0.11 | 0.09 | 0.10 | 0.08 | 0.02 | 0.14 | 0.00 | 0.20 | 0.05 | 0.07 | 0.03 | 0.30 | 0.00 | 1.09 | 0.06 | 0.23 | 0.01 | 0.11 | 0.00 | 0.00 | 0.03 | 0.19 | 0.24 | 0.36 | 0.04 | 0.10 | 0.09 | 0.11 | 0.01 | 0.27 | 0.18 | 0.21 | 0.08 | 0.11 | 0.02 | 0.01 | 0.00 | 0.07 | 0.00 | 0.06 | 0.02 | 0.27 | 0.00 | 0.07 | 0.06 | 0.12 |
| SLC26A5 | ENSG00000170615 | 0.01 | 0.00 | 0.07 | 0.00 | 0.01 | 0.00 | 0.04 | 0.02 | 0.05 | 0.02 | 0.00 | 0.00 | 0.03 | 0.00 | 0.08 | 0.02 | 0.19 | 0.02 | 0.20 | 0.01 | 0.44 | 0.04 | 0.18 | 0.03 | 0.02 | 0.01 | 0.01 | 0.00 | 0.02 | 0.02 | 0.06 | 0.02 | 0.00 | 0.02 | 0.02 | 0.06 | 0.00 | 0.01 | 0.00 | 0.00 | 0.05 | 0.04 | 0.26 | 0.06 | 0.04 | 0.02 | 0.05 | 0.03 | 0.09 | 0.05 | 0.08 | 0.05 | 0.08 | 0.01 | 0.00 | 0.00 | 0.13 | 0.00 | 0.07 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.06 | 0.04 |
| CNGB3 | ENSG00000170289 | 0.00 | 0.00 | 0.00 | 0.01 | 0.06 | 0.00 | 0.07 | 0.03 | 0.15 | 0.01 | 0.00 | 0.00 | 0.02 | 0.01 | 0.16 | 0.02 | 0.13 | 0.03 | 0.06 | 0.01 | 0.16 | 0.00 | 0.14 | 0.00 | 0.09 | 0.00 | 0.12 | 0.02 | 0.02 | 0.02 | 0.15 | 0.00 | 0.20 | 0.01 | 0.06 | 0.00 | 0.02 | 0.02 | 0.00 | 0.00 | 0.29 | 0.01 | 0.30 | 0.11 | 0.05 | 0.01 | 0.05 | 0.01 | 0.19 | 0.04 | 0.21 | 0.07 | 0.16 | 0.00 | 0.00 | 0.00 | 0.04 | 0.02 | 0.03 | 0.00 | 0.01 | 0.01 | 0.25 | 0.00 | 0.09 | 0.01 |
| GADL1 | ENSG00000144644 | 0.00 | 0.17 | 0.00 | 0.01 | 0.10 | 0.00 | 0.02 | 0.02 | 0.16 | 0.03 | 0.00 | 0.03 | 0.02 | 0.18 | 0.01 | 0.04 | 0.01 | 0.05 | 0.00 | 0.05 | 0.03 | 0.04 | 0.05 | 0.09 | 0.00 | 0.03 | 0.03 | 0.02 | 0.01 | 0.02 | 0.06 | 0.01 | 0.00 | 0.16 | 0.05 | 0.01 | 0.01 | 0.05 | 0.00 | 0.00 | 0.06 | 0.05 | 0.11 | 0.18 | 0.03 | 0.05 | 0.04 | 0.03 | 0.10 | 0.09 | 0.13 | 0.03 | 0.05 | 0.04 | 0.00 | 0.01 | 0.04 | 0.06 | 0.03 | 0.01 | 0.00 | 0.02 | 0.00 | 0.03 | 0.03 | 0.04 |
| KSR2 | ENSG00000171435 | 0.01 | 0.01 | 0.02 | 0.00 | 0.06 | 0.02 | 0.05 | 0.03 | 0.15 | 0.03 | 0.00 | 0.00 | 0.03 | 0.00 | 0.03 | 0.05 | 0.03 | 0.05 | 0.03 | 0.03 | 0.08 | 0.05 | 0.06 | 0.02 | 0.01 | 0.01 | 0.04 | 0.02 | 0.01 | 0.07 | 0.04 | 0.05 | 0.00 | 0.22 | 0.15 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.04 | 0.08 | 0.14 | 0.20 | 0.04 | 0.02 | 0.02 | 0.05 | 0.25 | 0.08 | 0.28 | 0.06 | 0.01 | 0.00 | 0.00 | 0.01 | 0.10 | 0.00 | 0.03 | 0.01 | 0.03 | 0.00 | 0.00 | 0.00 | 0.03 | 0.07 |
| HCRTR2 | ENSG00000137252 | 0.00 | 0.00 | 0.02 | 0.02 | 0.00 | 0.00 | 0.00 | 0.02 | 0.09 | 0.04 | 0.00 | 0.00 | 0.01 | 0.00 | 0.07 | 0.02 | 0.26 | 0.05 | 0.14 | 0.01 | 0.28 | 0.04 | 0.11 | 0.01 | 0.03 | 0.01 | 0.08 | 0.02 | 0.03 | 0.00 | 0.06 | 0.00 | 0.00 | 0.05 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.11 | 0.03 | 0.16 | 0.05 | 0.08 | 0.04 | 0.05 | 0.01 | 0.20 | 0.03 | 0.10 | 0.05 | 0.03 | 0.00 | 0.00 | 0.00 | 0.09 | 0.00 | 0.02 | 0.00 | 0.01 | 0.01 | 0.01 | 0.00 | 0.06 | 0.02 |
| LCT | ENSG00000115850 | 0.01 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.18 | 0.04 | 0.04 | 0.00 | 0.01 | 0.00 | 0.01 | 0.02 | 0.02 | 0.07 | 0.03 | 0.04 | 0.01 | 0.08 | 0.07 | 0.03 | 0.06 | 0.00 | 0.02 | 0.01 | 0.02 | 0.01 | 0.01 | 0.02 | 0.04 | 0.05 | 0.03 | 0.06 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.06 | 0.09 | 0.16 | 0.02 | 0.02 | 0.04 | 0.01 | 0.07 | 0.00 | 0.12 | 0.04 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.13 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 |
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