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 |
| OLFM2 | ENSG00000105088 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.08 | 0.04 | 0.00 | 0.01 | 0.14 | 0.02 | 0.02 | 0.04 | 0.07 | 0.06 | 0.05 | 0.05 | 0.03 | 0.06 | 0.03 | 0.05 | 0.01 | 0.01 | 0.01 | 0.04 | 0.01 | 0.02 | 0.01 | 0.11 | 0.00 | 0.01 | 0.10 | 0.03 | 0.01 | 0.00 | 0.00 | 0.01 | 0.09 | 0.05 | 0.53 | 0.22 | 0.11 | 0.06 | 0.17 | 0.11 | 0.61 | 0.23 | 0.34 | 0.02 | 0.02 | 0.00 | 0.03 | 0.00 | 0.00 | 0.03 | 0.01 | 0.00 | 0.05 | 0.01 | 0.00 | 0.02 | 0.02 | 0.01 |
| PLSCR4 | ENSG00000114698 | 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 | 0.08 | 0.01 | 0.66 | 0.01 | 0.34 | 0.00 | 0.39 | 0.01 | 0.09 | 0.01 | 0.01 | 0.00 | 0.05 | 0.01 | 0.00 | 0.00 | 0.07 | 0.01 | 0.03 | 0.03 | 0.09 | 0.01 | 0.00 | 0.05 | 0.00 | 0.00 | 0.12 | 0.02 | 0.60 | 0.02 | 0.37 | 0.01 | 0.12 | 0.01 | 0.24 | 0.02 | 0.05 | 0.07 | 0.05 | 0.00 | 0.00 | 0.00 | 0.01 | 0.05 | 0.00 | 0.01 | 0.02 | 0.03 | 0.00 | 0.00 | 0.02 | 0.04 |
| HDAC10 | ENSG00000100429 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.03 | 0.01 | 0.03 | 0.01 | 0.12 | 0.00 | 0.03 | 0.00 | 0.06 | 0.02 | 0.12 | 0.06 | 0.09 | 0.02 | 0.04 | 0.03 | 0.03 | 0.03 | 0.07 | 0.00 | 0.04 | 0.01 | 0.09 | 0.01 | 0.10 | 0.07 | 0.07 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.06 | 0.00 | 0.01 | 0.06 | 0.06 | 0.02 | 0.64 | 0.03 | 0.07 | 0.03 | 0.15 | 0.06 | 0.27 | 0.06 | 0.15 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.09 | 0.00 | 0.05 | 0.00 | 0.10 | 0.00 | 0.00 | 0.12 | 0.05 |
| PRKCH | ENSG00000027075 | 0.00 | 0.02 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.04 | 0.03 | 0.05 | 0.00 | 0.01 | 0.00 | 0.03 | 0.06 | 0.03 | 0.03 | 0.05 | 0.08 | 0.02 | 0.06 | 0.03 | 0.07 | 0.03 | 0.00 | 0.03 | 0.03 | 0.03 | 0.01 | 0.00 | 0.01 | 0.07 | 0.00 | 0.29 | 0.00 | 0.03 | 0.01 | 0.03 | 0.00 | 0.00 | 0.05 | 0.07 | 0.08 | 0.25 | 0.03 | 0.01 | 0.02 | 0.02 | 0.13 | 0.13 | 0.03 | 0.10 | 0.00 | 0.01 | 0.00 | 0.00 | 0.04 | 0.00 | 0.02 | 0.08 | 0.01 | 0.07 | 0.03 | 0.00 | 0.01 | 0.05 |
| NOTCH3 | ENSG00000074181 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.03 | 0.04 | 0.00 | 0.00 | 0.06 | 0.00 | 0.01 | 0.02 | 0.13 | 0.03 | 0.06 | 0.02 | 0.23 | 0.02 | 0.06 | 0.00 | 0.02 | 0.00 | 0.02 | 0.01 | 0.01 | 0.00 | 0.08 | 0.03 | 0.00 | 0.03 | 0.34 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.15 | 0.03 | 0.89 | 0.05 | 0.03 | 0.03 | 0.26 | 0.01 | 0.50 | 0.05 | 0.19 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.02 | 0.00 | 0.03 | 0.00 | 0.02 | 0.00 | 0.04 | 0.01 |
| ALOX12 | ENSG00000108839 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.18 | 0.04 | 0.03 | 0.00 | 0.02 | 0.00 | 0.02 | 0.01 | 0.05 | 0.01 | 0.02 | 0.01 | 0.03 | 0.03 | 0.03 | 0.01 | 0.02 | 0.00 | 0.02 | 0.00 | 0.05 | 0.02 | 0.03 | 0.00 | 0.15 | 0.03 | 0.08 | 0.02 | 0.08 | 0.00 | 0.03 | 0.00 | 0.00 | 0.01 | 0.08 | 0.11 | 0.04 | 0.01 | 0.03 | 0.04 | 0.03 | 0.06 | 0.24 | 0.10 | 0.36 | 0.00 | 0.02 | 0.00 | 0.01 | 0.00 | 0.06 | 0.00 | 0.01 | 0.00 | 0.07 | 0.00 | 0.00 | 0.02 | 0.04 |
| GPR68 | ENSG00000119714 | 0.00 | 0.02 | 0.01 | 0.01 | 0.00 | 0.04 | 0.02 | 0.04 | 0.10 | 0.05 | 0.00 | 0.00 | 0.00 | 0.05 | 0.06 | 0.05 | 0.11 | 0.03 | 0.04 | 0.05 | 0.08 | 0.07 | 0.03 | 0.04 | 0.01 | 0.04 | 0.01 | 0.02 | 0.01 | 0.01 | 0.01 | 0.09 | 0.00 | 0.31 | 0.05 | 0.00 | 0.02 | 0.01 | 0.00 | 0.00 | 0.03 | 0.09 | 0.21 | 0.16 | 0.07 | 0.09 | 0.04 | 0.02 | 0.06 | 0.05 | 0.05 | 0.11 | 0.03 | 0.01 | 0.00 | 0.00 | 0.03 | 0.00 | 0.00 | 0.10 | 0.02 | 0.06 | 0.03 | 0.01 | 0.01 | 0.06 |
| NRP1 | ENSG00000099250 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.04 | 0.05 | 0.00 | 0.01 | 0.03 | 0.02 | 0.08 | 0.01 | 0.05 | 0.01 | 0.05 | 0.02 | 0.14 | 0.01 | 0.12 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.06 | 0.01 | 0.03 | 0.01 | 0.03 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.02 | 0.20 | 0.04 | 0.01 | 0.01 | 0.02 | 0.01 | 0.22 | 0.00 | 0.04 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.02 |
| ABCA13 | ENSG00000179869 | 0.00 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 | 0.06 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.09 | 0.01 | 0.12 | 0.04 | 0.12 | 0.01 | 0.17 | 0.03 | 0.06 | 0.01 | 0.02 | 0.00 | 0.01 | 0.01 | 0.02 | 0.00 | 0.03 | 0.00 | 0.00 | 0.01 | 0.07 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.06 | 0.03 | 0.12 | 0.06 | 0.02 | 0.00 | 0.04 | 0.02 | 0.04 | 0.00 | 0.05 | 0.03 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.05 | 0.02 | 0.00 | 0.09 | 0.01 | 0.00 | 0.00 | 0.04 | 0.03 |
| ADCY3 | ENSG00000138031 | 0.00 | 0.00 | 0.02 | 0.02 | 0.00 | 0.00 | 0.02 | 0.01 | 0.08 | 0.01 | 0.00 | 0.00 | 0.03 | 0.08 | 0.05 | 0.01 | 0.09 | 0.02 | 0.03 | 0.02 | 0.05 | 0.05 | 0.03 | 0.03 | 0.01 | 0.00 | 0.01 | 0.02 | 0.01 | 0.04 | 0.09 | 0.01 | 0.00 | 0.05 | 0.01 | 0.04 | 0.01 | 0.00 | 0.00 | 0.00 | 0.05 | 0.04 | 0.17 | 0.11 | 0.08 | 0.00 | 0.11 | 0.02 | 0.30 | 0.03 | 0.04 | 0.11 | 0.17 | 0.01 | 0.00 | 0.01 | 0.02 | 0.06 | 0.00 | 0.01 | 0.02 | 0.04 | 0.05 | 0.00 | 0.03 | 0.04 |
| PBRM1 | ENSG00000163939 | 0.00 | 0.18 | 0.00 | 0.03 | 0.00 | 0.02 | 0.00 | 0.03 | 0.04 | 0.16 | 0.00 | 0.03 | 0.00 | 0.64 | 0.02 | 0.06 | 0.01 | 0.11 | 0.00 | 0.06 | 0.03 | 0.13 | 0.02 | 0.13 | 0.00 | 0.06 | 0.02 | 0.07 | 0.00 | 0.05 | 0.03 | 0.08 | 0.00 | 0.20 | 0.15 | 0.01 | 0.00 | 0.04 | 0.00 | 0.00 | 0.01 | 0.17 | 0.08 | 0.22 | 0.00 | 0.07 | 0.08 | 0.07 | 0.05 | 0.30 | 0.04 | 0.15 | 0.05 | 0.01 | 0.00 | 0.01 | 0.00 | 0.06 | 0.01 | 0.06 | 0.02 | 0.05 | 0.00 | 0.03 | 0.02 | 0.04 |
| SPINK5 | ENSG00000133710 | 0.30 | 0.00 | 0.03 | 0.01 | 0.00 | 0.00 | 0.02 | 0.02 | 0.02 | 0.05 | 0.00 | 0.00 | 0.02 | 0.04 | 0.05 | 0.04 | 0.01 | 0.04 | 0.01 | 0.05 | 0.03 | 0.03 | 0.03 | 0.05 | 0.01 | 0.03 | 0.03 | 0.01 | 0.02 | 0.02 | 0.08 | 0.02 | 0.09 | 0.01 | 0.22 | 0.04 | 0.00 | 0.04 | 0.01 | 0.00 | 0.03 | 0.02 | 0.15 | 0.10 | 0.05 | 0.01 | 0.02 | 0.03 | 0.09 | 0.02 | 0.07 | 0.04 | 0.00 | 0.00 | 0.00 | 0.10 | 0.04 | 0.00 | 0.00 | 0.05 | 0.01 | 0.03 | 0.00 | 0.03 | 0.03 | 0.14 |
| NTRK1 | ENSG00000198400 | 0.03 | 0.00 | 0.01 | 0.01 | 0.00 | 0.03 | 0.01 | 0.05 | 0.33 | 0.01 | 0.02 | 0.00 | 0.11 | 0.00 | 0.28 | 0.00 | 0.23 | 0.00 | 0.06 | 0.00 | 0.24 | 0.00 | 0.13 | 0.00 | 0.03 | 0.00 | 0.11 | 0.01 | 0.07 | 0.00 | 0.32 | 0.00 | 0.43 | 0.01 | 0.14 | 0.02 | 0.07 | 0.00 | 0.00 | 0.01 | 0.27 | 0.01 | 0.44 | 0.02 | 0.16 | 0.00 | 0.17 | 0.00 | 0.50 | 0.01 | 0.39 | 0.02 | 0.10 | 0.00 | 0.00 | 0.00 | 0.25 | 0.00 | 0.05 | 0.00 | 0.07 | 0.00 | 0.00 | 0.00 | 0.16 | 0.01 |
| PRSS1 | ENSG00000204983 | 0.02 | 0.01 | 0.05 | 0.00 | 0.05 | 0.02 | 0.02 | 0.03 | 0.05 | 0.04 | 0.00 | 0.01 | 0.04 | 0.04 | 0.08 | 0.02 | 0.08 | 0.06 | 0.02 | 0.15 | 0.04 | 0.20 | 0.03 | 0.09 | 0.02 | 0.01 | 0.03 | 0.02 | 0.03 | 0.04 | 0.04 | 0.06 | 0.00 | 0.11 | 0.06 | 0.06 | 0.00 | 0.02 | 0.00 | 0.00 | 0.09 | 0.04 | 0.54 | 0.05 | 0.04 | 0.09 | 0.04 | 0.05 | 0.05 | 0.14 | 0.11 | 0.12 | 0.02 | 0.04 | 0.00 | 0.05 | 0.02 | 0.09 | 0.10 | 0.00 | 0.04 | 0.02 | 0.00 | 0.03 | 0.21 | 0.02 |
| PPIL6 | ENSG00000185250 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.30 | 0.02 | 0.13 | 0.00 | 0.01 | 0.00 | 0.14 | 0.03 | 0.06 | 0.05 | 0.05 | 0.02 | 0.03 | 0.05 | 0.07 | 0.05 | 0.07 | 0.01 | 0.03 | 0.01 | 0.04 | 0.00 | 0.03 | 0.01 | 0.08 | 0.00 | 0.15 | 0.15 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.15 | 0.10 | 0.10 | 0.24 | 0.04 | 0.02 | 0.06 | 0.02 | 0.11 | 0.03 | 0.12 | 0.08 | 0.00 | 0.04 | 0.00 | 0.00 | 0.01 | 0.25 | 0.00 | 0.02 | 0.02 | 0.05 | 0.06 | 0.03 | 0.01 | 0.12 |
| MAK | ENSG00000111837 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.03 | 0.26 | 0.08 | 0.00 | 0.02 | 0.01 | 0.02 | 0.09 | 0.01 | 0.11 | 0.07 | 0.04 | 0.06 | 0.18 | 0.19 | 0.04 | 0.10 | 0.02 | 0.04 | 0.02 | 0.04 | 0.04 | 0.07 | 0.13 | 0.01 | 0.06 | 0.03 | 0.05 | 0.03 | 0.00 | 0.01 | 0.00 | 0.00 | 0.17 | 0.04 | 0.51 | 0.08 | 0.10 | 0.06 | 0.09 | 0.02 | 0.19 | 0.05 | 0.10 | 0.13 | 0.04 | 0.03 | 0.00 | 0.00 | 0.10 | 0.04 | 0.01 | 0.03 | 0.01 | 0.03 | 0.28 | 0.00 | 0.26 | 0.00 |
| COL9A2 | ENSG00000049089 | 0.01 | 0.02 | 0.01 | 0.03 | 0.00 | 0.00 | 0.01 | 0.01 | 0.30 | 0.02 | 0.00 | 0.00 | 0.11 | 0.03 | 0.13 | 0.02 | 0.14 | 0.02 | 0.08 | 0.02 | 0.30 | 0.02 | 0.07 | 0.03 | 0.03 | 0.02 | 0.02 | 0.03 | 0.04 | 0.01 | 0.03 | 0.10 | 0.00 | 0.26 | 0.00 | 0.03 | 0.03 | 0.07 | 0.00 | 0.00 | 0.07 | 0.05 | 0.72 | 0.05 | 0.07 | 0.01 | 0.14 | 0.01 | 0.22 | 0.05 | 0.11 | 0.04 | 0.04 | 0.03 | 0.02 | 0.00 | 0.00 | 0.03 | 0.00 | 0.01 | 0.03 | 0.02 | 0.00 | 0.10 | 0.05 | 0.02 |
| NCEH1 | ENSG00000144959 | 0.05 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.08 | 0.01 | 0.18 | 0.01 | 0.00 | 0.00 | 0.00 | 0.03 | 0.19 | 0.02 | 1.76 | 0.00 | 0.62 | 0.00 | 0.87 | 0.00 | 0.27 | 0.01 | 0.03 | 0.01 | 0.04 | 0.01 | 0.04 | 0.00 | 0.20 | 0.01 | 0.12 | 0.01 | 0.10 | 0.00 | 0.00 | 0.08 | 0.00 | 0.00 | 0.23 | 0.01 | 1.35 | 0.02 | 0.74 | 0.00 | 0.45 | 0.01 | 1.09 | 0.04 | 0.06 | 0.07 | 0.20 | 0.00 | 0.00 | 0.00 | 0.06 | 0.00 | 0.03 | 0.00 | 0.06 | 0.02 | 0.00 | 0.00 | 0.02 | 0.03 |
| SFRP5 | ENSG00000120057 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.11 | 0.02 | 0.09 | 0.00 | 0.02 | 0.00 | 0.18 | 0.01 | 0.03 | 0.02 | 0.07 | 0.00 | 0.05 | 0.02 | 0.09 | 0.02 | 0.09 | 0.00 | 0.09 | 0.00 | 0.06 | 0.01 | 0.03 | 0.03 | 0.06 | 0.16 | 0.14 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.01 | 0.03 | 0.08 | 0.07 | 0.33 | 0.01 | 0.07 | 0.02 | 0.09 | 0.04 | 0.09 | 0.02 | 0.05 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.07 | 0.00 | 0.04 | 0.01 | 0.05 | 0.00 | 0.00 | 0.02 | 0.04 |
| MTA1 | ENSG00000182979 | 0.00 | 0.02 | 0.01 | 0.01 | 0.01 | 0.04 | 0.02 | 0.03 | 0.08 | 0.07 | 0.00 | 0.00 | 0.00 | 0.07 | 0.06 | 0.07 | 0.21 | 0.03 | 0.07 | 0.05 | 0.10 | 0.08 | 0.03 | 0.08 | 0.01 | 0.03 | 0.03 | 0.04 | 0.02 | 0.02 | 0.01 | 0.14 | 0.04 | 0.31 | 0.16 | 0.00 | 0.01 | 0.03 | 0.00 | 0.00 | 0.07 | 0.07 | 0.37 | 0.17 | 0.07 | 0.08 | 0.09 | 0.03 | 0.10 | 0.05 | 0.15 | 0.06 | 0.03 | 0.01 | 0.00 | 0.00 | 0.08 | 0.03 | 0.01 | 0.07 | 0.02 | 0.05 | 0.03 | 0.03 | 0.01 | 0.07 |
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