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 |
| STAT1 | ENSG00000115415 | 0.02 | 0.02 | 0.10 | 0.00 | 0.00 | 0.01 | 0.01 | 0.02 | 0.07 | 0.07 | 0.00 | 0.00 | 0.00 | 0.02 | 0.04 | 0.01 | 0.15 | 0.06 | 0.18 | 0.05 | 0.16 | 0.02 | 0.08 | 0.03 | 0.01 | 0.00 | 0.02 | 0.01 | 0.07 | 0.01 | 0.07 | 0.02 | 0.00 | 0.01 | 0.02 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.09 | 0.02 | 0.41 | 0.04 | 0.12 | 0.03 | 0.07 | 0.01 | 0.05 | 0.03 | 0.08 | 0.07 | 0.06 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.02 |
| SLCO2B1 | ENSG00000137491 | 0.00 | 0.01 | 0.00 | 0.00 | 0.10 | 0.00 | 0.04 | 0.00 | 0.17 | 0.03 | 0.00 | 0.00 | 0.08 | 0.00 | 0.13 | 0.01 | 0.15 | 0.02 | 0.24 | 0.03 | 0.54 | 0.02 | 0.13 | 0.01 | 0.02 | 0.00 | 0.03 | 0.02 | 0.01 | 0.01 | 0.08 | 0.02 | 0.02 | 0.02 | 0.03 | 0.00 | 0.02 | 0.02 | 0.00 | 0.00 | 0.43 | 0.06 | 0.54 | 0.02 | 0.10 | 0.01 | 0.11 | 0.02 | 0.14 | 0.16 | 0.19 | 0.05 | 0.02 | 0.03 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.23 | 0.01 |
| NPEPPS | ENSG00000141279 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.04 | 0.12 | 0.01 | 0.00 | 0.00 | 0.08 | 0.01 | 0.07 | 0.00 | 0.09 | 0.02 | 0.02 | 0.01 | 0.09 | 0.03 | 0.06 | 0.01 | 0.02 | 0.01 | 0.05 | 0.03 | 0.04 | 0.02 | 0.02 | 0.02 | 0.02 | 0.01 | 0.03 | 0.04 | 0.01 | 0.06 | 0.00 | 0.00 | 0.14 | 0.07 | 0.10 | 0.08 | 0.05 | 0.01 | 0.04 | 0.06 | 0.21 | 0.19 | 0.08 | 0.03 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.01 | 0.03 | 0.03 | 0.06 | 0.04 |
| PHF21A | ENSG00000135365 | 0.01 | 0.00 | 0.00 | 0.00 | 0.05 | 0.00 | 0.00 | 0.08 | 0.04 | 0.04 | 0.00 | 0.01 | 0.00 | 0.01 | 0.05 | 0.02 | 0.15 | 0.03 | 0.12 | 0.01 | 0.15 | 0.03 | 0.16 | 0.01 | 0.01 | 0.00 | 0.01 | 0.00 | 0.04 | 0.02 | 0.02 | 0.00 | 0.00 | 0.07 | 0.06 | 0.01 | 0.01 | 0.03 | 0.00 | 0.00 | 0.07 | 0.02 | 0.13 | 0.06 | 0.07 | 0.02 | 0.06 | 0.02 | 0.03 | 0.03 | 0.11 | 0.07 | 0.00 | 0.04 | 0.01 | 0.00 | 0.00 | 0.05 | 0.01 | 0.02 | 0.01 | 0.06 | 0.00 | 0.02 | 0.02 | 0.05 |
| CA10 | ENSG00000154975 | 0.01 | 0.00 | 0.05 | 0.00 | 0.00 | 0.00 | 0.03 | 0.02 | 0.14 | 0.02 | 0.00 | 0.00 | 0.11 | 0.00 | 0.10 | 0.00 | 0.11 | 0.01 | 0.03 | 0.01 | 0.21 | 0.00 | 0.10 | 0.01 | 0.03 | 0.01 | 0.08 | 0.04 | 0.07 | 0.05 | 0.09 | 0.01 | 0.02 | 0.01 | 0.02 | 0.03 | 0.02 | 0.01 | 0.00 | 0.00 | 0.42 | 0.04 | 0.14 | 0.04 | 0.09 | 0.01 | 0.08 | 0.02 | 0.14 | 0.02 | 0.17 | 0.01 | 0.02 | 0.00 | 0.00 | 0.00 | 0.05 | 0.00 | 0.03 | 0.01 | 0.02 | 0.01 | 0.05 | 0.03 | 0.18 | 0.02 |
| AGXT2 | ENSG00000113492 | 0.00 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.02 | 0.02 | 0.13 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.18 | 0.00 | 0.20 | 0.00 | 0.07 | 0.00 | 0.10 | 0.01 | 0.13 | 0.02 | 0.05 | 0.01 | 0.04 | 0.00 | 0.02 | 0.01 | 0.07 | 0.00 | 0.00 | 0.01 | 0.30 | 0.00 | 0.01 | 0.02 | 0.00 | 0.00 | 0.07 | 0.02 | 0.22 | 0.02 | 0.07 | 0.00 | 0.07 | 0.01 | 0.15 | 0.03 | 0.25 | 0.02 | 0.00 | 0.02 | 0.00 | 0.00 | 0.02 | 0.00 | 0.01 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.13 | 0.02 |
| CYP39A1 | ENSG00000146233 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.02 | 0.02 | 0.12 | 0.04 | 0.00 | 0.00 | 0.01 | 0.02 | 0.11 | 0.01 | 0.16 | 0.04 | 0.06 | 0.02 | 0.28 | 0.03 | 0.18 | 0.02 | 0.05 | 0.00 | 0.11 | 0.01 | 0.02 | 0.00 | 0.08 | 0.00 | 0.05 | 0.03 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.10 | 0.03 | 0.22 | 0.07 | 0.06 | 0.03 | 0.05 | 0.01 | 0.03 | 0.03 | 0.11 | 0.03 | 0.02 | 0.01 | 0.00 | 0.00 | 0.09 | 0.02 | 0.01 | 0.00 | 0.00 | 0.03 | 0.02 | 0.00 | 0.07 | 0.01 |
| PRKD1 | ENSG00000184304 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.01 | 0.05 | 0.07 | 0.00 | 0.00 | 0.00 | 0.02 | 0.34 | 0.03 | 0.10 | 0.05 | 0.05 | 0.06 | 0.16 | 0.04 | 0.07 | 0.03 | 0.03 | 0.02 | 0.02 | 0.06 | 0.00 | 0.01 | 0.06 | 0.02 | 0.00 | 0.02 | 0.15 | 0.05 | 0.00 | 0.01 | 0.00 | 0.00 | 0.14 | 0.03 | 0.21 | 0.13 | 0.04 | 0.01 | 0.05 | 0.03 | 0.11 | 0.07 | 0.20 | 0.04 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.03 | 0.01 | 0.09 | 0.00 | 0.00 | 0.03 | 0.02 |
| GUCY2C | ENSG00000070019 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.11 | 0.02 | 0.06 | 0.01 | 0.00 | 0.00 | 0.06 | 0.03 | 0.09 | 0.08 | 0.02 | 0.05 | 0.03 | 0.13 | 0.04 | 0.04 | 0.08 | 0.01 | 0.03 | 0.00 | 0.07 | 0.01 | 0.07 | 0.01 | 0.05 | 0.14 | 0.05 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.06 | 0.07 | 0.25 | 0.13 | 0.01 | 0.03 | 0.03 | 0.02 | 0.09 | 0.03 | 0.20 | 0.14 | 0.56 | 0.00 | 0.00 | 0.05 | 0.00 | 0.04 | 0.03 | 0.02 | 0.00 | 0.06 | 0.00 | 0.01 | 0.04 | 0.02 |
| AEBP1 | ENSG00000106624 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.06 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.01 | 0.09 | 0.02 | 0.03 | 0.01 | 0.10 | 0.03 | 0.05 | 0.01 | 0.03 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.04 | 0.00 | 0.00 | 0.01 | 0.11 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.08 | 0.01 | 0.10 | 0.06 | 0.02 | 0.00 | 0.03 | 0.01 | 0.08 | 0.00 | 0.05 | 0.02 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.02 | 0.01 | 0.00 | 0.05 | 0.01 | 0.00 | 0.00 | 0.03 | 0.03 |
| SLC9A9 | ENSG00000181804 | 0.03 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.06 | 0.02 | 0.09 | 0.01 | 0.00 | 0.00 | 0.00 | 0.03 | 0.06 | 0.01 | 0.56 | 0.01 | 0.31 | 0.01 | 0.39 | 0.02 | 0.11 | 0.01 | 0.01 | 0.01 | 0.05 | 0.00 | 0.01 | 0.00 | 0.08 | 0.01 | 0.00 | 0.03 | 0.09 | 0.01 | 0.01 | 0.05 | 0.00 | 0.00 | 0.11 | 0.02 | 0.55 | 0.02 | 0.36 | 0.01 | 0.12 | 0.01 | 0.24 | 0.02 | 0.10 | 0.08 | 0.03 | 0.01 | 0.00 | 0.00 | 0.04 | 0.02 | 0.00 | 0.01 | 0.02 | 0.03 | 0.00 | 0.00 | 0.00 | 0.04 |
| CTSS | ENSG00000163131 | 0.03 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.07 | 0.00 | 0.64 | 0.01 | 0.02 | 0.00 | 0.11 | 0.02 | 0.45 | 0.01 | 0.31 | 0.00 | 0.09 | 0.01 | 0.24 | 0.00 | 0.24 | 0.00 | 0.03 | 0.00 | 0.17 | 0.00 | 0.06 | 0.00 | 0.44 | 0.01 | 0.43 | 0.01 | 0.25 | 0.00 | 0.10 | 0.00 | 0.00 | 0.00 | 0.43 | 0.00 | 0.78 | 0.02 | 0.22 | 0.00 | 0.33 | 0.00 | 0.54 | 0.00 | 0.47 | 0.02 | 0.13 | 0.00 | 0.00 | 0.00 | 0.28 | 0.00 | 0.01 | 0.00 | 0.06 | 0.00 | 0.00 | 0.00 | 0.21 | 0.01 |
| ANTXR1 | ENSG00000169604 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.04 | 0.11 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.03 | 0.01 | 0.18 | 0.00 | 0.05 | 0.00 | 0.12 | 0.00 | 0.05 | 0.01 | 0.00 | 0.01 | 0.02 | 0.01 | 0.00 | 0.01 | 0.02 | 0.03 | 0.06 | 0.08 | 0.04 | 0.04 | 0.01 | 0.01 | 0.00 | 0.00 | 0.06 | 0.01 | 0.16 | 0.04 | 0.03 | 0.00 | 0.05 | 0.01 | 0.13 | 0.00 | 0.05 | 0.05 | 0.03 | 0.05 | 0.00 | 0.00 | 0.04 | 0.02 | 0.02 | 0.01 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.01 |
| SLC26A9 | ENSG00000174502 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.03 | 0.02 | 0.07 | 0.06 | 0.01 | 0.00 | 0.10 | 0.00 | 0.12 | 0.01 | 0.09 | 0.01 | 0.05 | 0.00 | 0.17 | 0.07 | 0.05 | 0.01 | 0.04 | 0.00 | 0.12 | 0.02 | 0.00 | 0.00 | 0.18 | 0.01 | 0.18 | 0.02 | 0.03 | 0.03 | 0.01 | 0.00 | 0.00 | 0.00 | 0.27 | 0.01 | 0.27 | 0.09 | 0.08 | 0.00 | 0.15 | 0.01 | 0.38 | 0.04 | 0.06 | 0.18 | 0.05 | 0.02 | 0.01 | 0.00 | 0.21 | 0.04 | 0.00 | 0.01 | 0.04 | 0.02 | 0.09 | 0.00 | 0.17 | 0.02 |
| SLC4A7 | ENSG00000033867 | 0.01 | 0.18 | 0.00 | 0.01 | 0.09 | 0.00 | 0.00 | 0.02 | 0.17 | 0.04 | 0.00 | 0.03 | 0.02 | 0.09 | 0.01 | 0.04 | 0.01 | 0.04 | 0.00 | 0.05 | 0.04 | 0.04 | 0.04 | 0.06 | 0.00 | 0.03 | 0.03 | 0.02 | 0.02 | 0.02 | 0.05 | 0.01 | 0.00 | 0.11 | 0.05 | 0.01 | 0.01 | 0.03 | 0.00 | 0.00 | 0.06 | 0.05 | 0.11 | 0.17 | 0.03 | 0.02 | 0.04 | 0.02 | 0.12 | 0.11 | 0.11 | 0.02 | 0.05 | 0.04 | 0.00 | 0.01 | 0.04 | 0.01 | 0.02 | 0.01 | 0.00 | 0.02 | 0.00 | 0.03 | 0.05 | 0.04 |
| AOC1 | ENSG00000002726 | 0.03 | 0.01 | 0.04 | 0.00 | 0.05 | 0.02 | 0.03 | 0.03 | 0.05 | 0.05 | 0.00 | 0.01 | 0.00 | 0.04 | 0.10 | 0.02 | 0.09 | 0.09 | 0.02 | 0.17 | 0.07 | 0.26 | 0.02 | 0.11 | 0.02 | 0.01 | 0.01 | 0.02 | 0.02 | 0.05 | 0.07 | 0.05 | 0.00 | 0.11 | 0.07 | 0.07 | 0.00 | 0.03 | 0.00 | 0.00 | 0.07 | 0.07 | 0.53 | 0.08 | 0.03 | 0.09 | 0.04 | 0.06 | 0.07 | 0.19 | 0.10 | 0.15 | 0.01 | 0.05 | 0.00 | 0.06 | 0.02 | 0.09 | 0.10 | 0.01 | 0.05 | 0.01 | 0.00 | 0.03 | 0.19 | 0.03 |
| TDRD10 | ENSG00000163239 | 0.03 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.07 | 0.00 | 0.38 | 0.01 | 0.02 | 0.00 | 0.11 | 0.00 | 0.37 | 0.00 | 0.26 | 0.00 | 0.05 | 0.00 | 0.23 | 0.00 | 0.18 | 0.01 | 0.03 | 0.00 | 0.11 | 0.00 | 0.09 | 0.00 | 0.36 | 0.00 | 0.49 | 0.01 | 0.21 | 0.00 | 0.10 | 0.00 | 0.00 | 0.00 | 0.31 | 0.00 | 0.49 | 0.02 | 0.20 | 0.00 | 0.18 | 0.00 | 0.53 | 0.00 | 0.40 | 0.01 | 0.10 | 0.00 | 0.00 | 0.00 | 0.25 | 0.00 | 0.02 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.22 | 0.01 |
| GBE1 | ENSG00000114480 | 0.00 | 0.05 | 0.04 | 0.01 | 0.00 | 0.02 | 0.01 | 0.07 | 0.06 | 0.14 | 0.00 | 0.03 | 0.00 | 0.08 | 0.04 | 0.06 | 0.04 | 0.19 | 0.01 | 0.11 | 0.04 | 0.21 | 0.03 | 0.05 | 0.02 | 0.01 | 0.02 | 0.05 | 0.00 | 0.03 | 0.01 | 0.08 | 0.00 | 0.17 | 0.10 | 0.01 | 0.00 | 0.04 | 0.00 | 0.00 | 0.02 | 0.11 | 0.09 | 0.12 | 0.03 | 0.13 | 0.02 | 0.07 | 0.06 | 0.34 | 0.17 | 0.06 | 0.08 | 0.00 | 0.00 | 0.02 | 0.02 | 0.00 | 0.00 | 0.02 | 0.00 | 0.02 | 0.00 | 0.00 | 0.09 | 0.02 |
| REG1A | ENSG00000115386 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.04 | 0.09 | 0.02 | 0.00 | 0.00 | 0.00 | 0.04 | 0.02 | 0.02 | 0.12 | 0.02 | 0.05 | 0.02 | 0.08 | 0.04 | 0.03 | 0.03 | 0.00 | 0.01 | 0.01 | 0.03 | 0.00 | 0.01 | 0.01 | 0.03 | 0.00 | 0.05 | 0.00 | 0.03 | 0.00 | 0.01 | 0.00 | 0.00 | 0.04 | 0.02 | 0.13 | 0.05 | 0.04 | 0.01 | 0.05 | 0.01 | 0.17 | 0.06 | 0.12 | 0.04 | 0.05 | 0.05 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.03 |
| MARK4 | ENSG00000007047 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.04 | 0.14 | 0.02 | 0.00 | 0.00 | 0.03 | 0.05 | 0.13 | 0.05 | 0.11 | 0.08 | 0.03 | 0.02 | 0.05 | 0.06 | 0.12 | 0.02 | 0.02 | 0.02 | 0.03 | 0.02 | 0.09 | 0.02 | 0.05 | 0.03 | 0.12 | 0.03 | 0.16 | 0.03 | 0.00 | 0.02 | 0.00 | 0.00 | 0.08 | 0.05 | 0.13 | 0.30 | 0.16 | 0.04 | 0.11 | 0.04 | 0.31 | 0.17 | 0.08 | 0.18 | 0.00 | 0.04 | 0.01 | 0.00 | 0.07 | 0.05 | 0.03 | 0.14 | 0.02 | 0.11 | 0.00 | 0.00 | 0.02 | 0.02 |
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