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 |
| METAP2 | ENSG00000111142 | 0.01 | 0.01 | 0.01 | 0.00 | 0.06 | 0.02 | 0.05 | 0.01 | 0.08 | 0.04 | 0.00 | 0.00 | 0.02 | 0.03 | 0.02 | 0.05 | 0.03 | 0.03 | 0.01 | 0.03 | 0.05 | 0.06 | 0.05 | 0.03 | 0.00 | 0.02 | 0.01 | 0.03 | 0.00 | 0.06 | 0.03 | 0.02 | 0.00 | 0.17 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.06 | 0.06 | 0.06 | 0.21 | 0.02 | 0.02 | 0.03 | 0.03 | 0.15 | 0.11 | 0.22 | 0.04 | 0.00 | 0.01 | 0.00 | 0.01 | 0.08 | 0.02 | 0.00 | 0.02 | 0.01 | 0.02 | 0.05 | 0.00 | 0.02 | 0.08 |
| SP100 | ENSG00000067066 | 0.01 | 0.07 | 0.04 | 0.04 | 0.00 | 0.05 | 0.01 | 0.02 | 0.00 | 0.31 | 0.00 | 0.03 | 0.00 | 0.07 | 0.04 | 0.04 | 0.02 | 0.20 | 0.01 | 0.19 | 0.04 | 0.16 | 0.03 | 0.05 | 0.02 | 0.03 | 0.02 | 0.02 | 0.07 | 0.01 | 0.03 | 0.05 | 0.00 | 0.01 | 0.03 | 0.06 | 0.00 | 0.01 | 0.00 | 0.01 | 0.02 | 0.09 | 0.15 | 0.19 | 0.02 | 0.36 | 0.03 | 0.05 | 0.13 | 0.06 | 0.03 | 0.35 | 0.05 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.07 | 0.00 | 0.01 | 0.04 | 0.05 | 0.01 | 0.09 |
| PHF3 | ENSG00000118482 | 0.00 | 0.01 | 0.02 | 0.01 | 0.00 | 0.00 | 0.01 | 0.10 | 0.13 | 0.06 | 0.00 | 0.00 | 0.02 | 0.05 | 0.09 | 0.05 | 0.26 | 0.04 | 0.14 | 0.02 | 0.20 | 0.04 | 0.14 | 0.04 | 0.04 | 0.01 | 0.07 | 0.00 | 0.01 | 0.02 | 0.16 | 0.03 | 0.04 | 0.23 | 0.05 | 0.02 | 0.00 | 0.04 | 0.00 | 0.00 | 0.11 | 0.06 | 0.17 | 0.10 | 0.09 | 0.02 | 0.04 | 0.01 | 0.08 | 0.05 | 0.09 | 0.08 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.04 | 0.00 | 0.02 | 0.01 | 0.03 | 0.05 | 0.03 | 0.16 | 0.03 |
| IL12RB1 | ENSG00000096996 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.03 | 0.00 | 0.03 | 0.05 | 0.01 | 0.03 | 0.02 | 0.09 | 0.02 | 0.05 | 0.02 | 0.11 | 0.01 | 0.04 | 0.02 | 0.01 | 0.00 | 0.01 | 0.04 | 0.01 | 0.02 | 0.09 | 0.03 | 0.06 | 0.03 | 0.09 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.09 | 0.02 | 0.53 | 0.04 | 0.02 | 0.02 | 0.19 | 0.03 | 0.30 | 0.07 | 0.07 | 0.02 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.01 | 0.01 | 0.02 | 0.00 | 0.03 | 0.01 |
| GNS | ENSG00000135677 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.02 | 0.14 | 0.02 | 0.00 | 0.00 | 0.03 | 0.00 | 0.19 | 0.01 | 0.17 | 0.02 | 0.16 | 0.01 | 0.22 | 0.02 | 0.17 | 0.02 | 0.01 | 0.00 | 0.02 | 0.04 | 0.06 | 0.02 | 0.03 | 0.01 | 0.13 | 0.01 | 0.25 | 0.03 | 0.05 | 0.00 | 0.00 | 0.00 | 0.15 | 0.02 | 0.20 | 0.05 | 0.05 | 0.01 | 0.01 | 0.01 | 0.30 | 0.07 | 0.29 | 0.06 | 0.02 | 0.00 | 0.00 | 0.01 | 0.12 | 0.00 | 0.03 | 0.02 | 0.07 | 0.06 | 0.00 | 0.00 | 0.08 | 0.02 |
| PRSS36 | ENSG00000178226 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.09 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.10 | 0.01 | 0.10 | 0.01 | 0.03 | 0.02 | 0.07 | 0.00 | 0.06 | 0.00 | 0.05 | 0.00 | 0.06 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.09 | 0.01 | 0.08 | 0.03 | 0.02 | 0.03 | 0.12 | 0.00 | 0.52 | 0.05 | 0.06 | 0.02 | 0.02 | 0.01 | 0.00 | 0.02 | 0.05 | 0.00 | 0.01 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.01 |
| ANGPTL1 | ENSG00000116194 | 0.02 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.03 | 0.23 | 0.01 | 0.02 | 0.00 | 0.09 | 0.01 | 0.11 | 0.00 | 0.18 | 0.01 | 0.03 | 0.00 | 0.17 | 0.03 | 0.11 | 0.01 | 0.03 | 0.00 | 0.13 | 0.00 | 0.05 | 0.00 | 0.16 | 0.00 | 0.17 | 0.01 | 0.00 | 0.04 | 0.02 | 0.00 | 0.00 | 0.00 | 0.16 | 0.01 | 0.35 | 0.03 | 0.08 | 0.01 | 0.10 | 0.00 | 0.25 | 0.00 | 0.20 | 0.03 | 0.08 | 0.00 | 0.00 | 0.00 | 0.32 | 0.00 | 0.01 | 0.00 | 0.01 | 0.01 | 0.02 | 0.00 | 0.10 | 0.03 |
| SCUBE1 | ENSG00000159307 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.02 | 0.00 | 0.04 | 0.02 | 0.08 | 0.00 | 0.03 | 0.00 | 0.04 | 0.04 | 0.06 | 0.06 | 0.03 | 0.02 | 0.02 | 0.04 | 0.01 | 0.02 | 0.03 | 0.00 | 0.02 | 0.01 | 0.06 | 0.02 | 0.06 | 0.04 | 0.05 | 0.00 | 0.05 | 0.00 | 0.00 | 0.00 | 0.06 | 0.00 | 0.00 | 0.05 | 0.05 | 0.01 | 0.40 | 0.04 | 0.06 | 0.03 | 0.08 | 0.10 | 0.29 | 0.04 | 0.08 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.08 | 0.02 | 0.04 | 0.00 | 0.08 | 0.00 | 0.00 | 0.23 | 0.01 |
| PTPRO | ENSG00000151490 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.09 | 0.02 | 0.05 | 0.01 | 0.00 | 0.00 | 0.06 | 0.05 | 0.10 | 0.09 | 0.02 | 0.05 | 0.03 | 0.13 | 0.04 | 0.05 | 0.07 | 0.02 | 0.04 | 0.02 | 0.07 | 0.02 | 0.06 | 0.01 | 0.04 | 0.14 | 0.05 | 0.01 | 0.00 | 0.01 | 0.01 | 0.00 | 0.01 | 0.07 | 0.06 | 0.24 | 0.13 | 0.01 | 0.03 | 0.03 | 0.02 | 0.07 | 0.03 | 0.10 | 0.13 | 0.57 | 0.00 | 0.00 | 0.05 | 0.00 | 0.04 | 0.04 | 0.02 | 0.01 | 0.06 | 0.00 | 0.01 | 0.04 | 0.03 |
| COL6A1 | ENSG00000142156 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.07 | 0.04 | 0.00 | 0.02 | 0.02 | 0.01 | 0.05 | 0.02 | 0.07 | 0.06 | 0.02 | 0.07 | 0.07 | 0.08 | 0.02 | 0.06 | 0.01 | 0.02 | 0.02 | 0.09 | 0.01 | 0.01 | 0.03 | 0.02 | 0.05 | 0.07 | 0.01 | 0.04 | 0.01 | 0.00 | 0.00 | 0.00 | 0.11 | 0.02 | 0.21 | 0.18 | 0.05 | 0.05 | 0.05 | 0.03 | 0.09 | 0.14 | 0.12 | 0.14 | 0.04 | 0.01 | 0.10 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.03 | 0.03 | 0.00 | 0.02 | 0.04 |
| TAB3 | ENSG00000157625 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.03 | 0.03 | 0.06 | 0.03 | 0.00 | 0.00 | 0.00 | 0.06 | 0.02 | 0.04 | 0.07 | 0.11 | 0.02 | 0.06 | 0.12 | 0.55 | 0.03 | 0.24 | 0.00 | 0.02 | 0.02 | 0.01 | 0.00 | 0.06 | 0.00 | 0.02 | 0.00 | 0.01 | 0.05 | 0.02 | 0.01 | 0.06 | 0.00 | 0.00 | 0.03 | 0.04 | 0.07 | 0.35 | 0.02 | 0.06 | 0.02 | 0.17 | 0.10 | 0.52 | 0.25 | 0.16 | 0.05 | 0.08 | 0.00 | 0.00 | 0.06 | 0.12 | 0.01 | 0.03 | 0.04 | 0.04 | 0.00 | 0.00 | 0.03 | 0.07 |
| FMOD | ENSG00000122176 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.05 | 0.06 | 0.02 | 0.00 | 0.10 | 0.00 | 0.13 | 0.00 | 0.11 | 0.01 | 0.05 | 0.01 | 0.19 | 0.06 | 0.08 | 0.01 | 0.04 | 0.00 | 0.12 | 0.01 | 0.00 | 0.00 | 0.19 | 0.01 | 0.18 | 0.02 | 0.04 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.27 | 0.00 | 0.31 | 0.07 | 0.06 | 0.01 | 0.11 | 0.01 | 0.17 | 0.00 | 0.09 | 0.12 | 0.05 | 0.00 | 0.01 | 0.00 | 0.26 | 0.02 | 0.06 | 0.01 | 0.23 | 0.00 | 0.09 | 0.00 | 0.18 | 0.01 |
| STK10 | ENSG00000072786 | 0.32 | 0.00 | 0.05 | 0.01 | 0.00 | 0.00 | 0.04 | 0.00 | 0.01 | 0.11 | 0.00 | 0.00 | 0.02 | 0.08 | 0.11 | 0.04 | 0.02 | 0.05 | 0.02 | 0.06 | 0.08 | 0.04 | 0.03 | 0.04 | 0.01 | 0.01 | 0.04 | 0.04 | 0.03 | 0.02 | 0.13 | 0.03 | 0.05 | 0.01 | 0.31 | 0.02 | 0.00 | 0.03 | 0.01 | 0.00 | 0.08 | 0.04 | 0.22 | 0.14 | 0.03 | 0.03 | 0.04 | 0.03 | 0.16 | 0.01 | 0.15 | 0.07 | 0.00 | 0.00 | 0.00 | 0.02 | 0.02 | 0.00 | 0.01 | 0.08 | 0.02 | 0.04 | 0.04 | 0.00 | 0.04 | 0.10 |
| NOTCH2 | ENSG00000134250 | 0.01 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.04 | 0.03 | 0.21 | 0.04 | 0.00 | 0.00 | 0.01 | 0.14 | 0.09 | 0.12 | 0.15 | 0.13 | 0.08 | 0.16 | 0.17 | 0.11 | 0.10 | 0.05 | 0.03 | 0.04 | 0.05 | 0.03 | 0.19 | 0.01 | 0.05 | 0.03 | 0.19 | 0.01 | 0.12 | 0.03 | 0.07 | 0.26 | 0.00 | 0.00 | 0.15 | 0.05 | 0.31 | 0.09 | 0.08 | 0.06 | 0.07 | 0.02 | 0.13 | 0.04 | 0.16 | 0.12 | 0.06 | 0.03 | 0.00 | 0.00 | 0.14 | 0.02 | 0.00 | 0.01 | 0.01 | 0.03 | 0.00 | 0.03 | 0.37 | 0.05 |
| PIP5K1C | ENSG00000186111 | 0.00 | 0.01 | 0.00 | 0.02 | 0.00 | 0.02 | 0.00 | 0.06 | 0.04 | 0.13 | 0.02 | 0.00 | 0.01 | 0.10 | 0.01 | 0.09 | 0.03 | 0.11 | 0.03 | 0.11 | 0.10 | 0.12 | 0.00 | 0.09 | 0.01 | 0.05 | 0.01 | 0.10 | 0.01 | 0.06 | 0.02 | 0.14 | 0.00 | 0.03 | 0.04 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.05 | 0.12 | 0.03 | 0.87 | 0.07 | 0.19 | 0.00 | 0.28 | 0.00 | 0.78 | 0.17 | 0.09 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 | 0.03 | 0.02 | 0.02 | 0.04 | 0.01 | 0.01 | 0.02 | 0.03 | 0.06 |
| LATS1 | ENSG00000131023 | 0.00 | 0.06 | 0.00 | 0.01 | 0.00 | 0.05 | 0.01 | 0.03 | 0.03 | 0.08 | 0.00 | 0.03 | 0.00 | 0.17 | 0.01 | 0.06 | 0.05 | 0.06 | 0.03 | 0.04 | 0.08 | 0.04 | 0.09 | 0.05 | 0.02 | 0.01 | 0.04 | 0.03 | 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 | 0.43 | 0.02 | 0.07 | 0.03 | 0.04 | 0.08 | 0.03 | 0.37 | 0.04 | 0.01 | 0.05 | 0.00 | 0.00 | 0.00 | 0.09 | 0.00 | 0.05 | 0.00 | 0.09 | 0.00 | 0.09 | 0.01 | 0.13 |
| THRB | ENSG00000151090 | 0.00 | 0.18 | 0.00 | 0.01 | 0.07 | 0.03 | 0.00 | 0.03 | 0.18 | 0.03 | 0.00 | 0.03 | 0.02 | 0.05 | 0.01 | 0.05 | 0.01 | 0.04 | 0.00 | 0.04 | 0.04 | 0.04 | 0.04 | 0.06 | 0.00 | 0.02 | 0.03 | 0.04 | 0.02 | 0.02 | 0.05 | 0.02 | 0.00 | 0.11 | 0.05 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.07 | 0.05 | 0.13 | 0.18 | 0.01 | 0.02 | 0.04 | 0.04 | 0.07 | 0.09 | 0.15 | 0.03 | 0.05 | 0.05 | 0.00 | 0.01 | 0.04 | 0.01 | 0.04 | 0.01 | 0.01 | 0.02 | 0.00 | 0.00 | 0.02 | 0.04 |
| KLK1 | ENSG00000167748 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.02 | 0.01 | 0.13 | 0.04 | 0.00 | 0.00 | 0.00 | 0.06 | 0.02 | 0.07 | 0.07 | 0.10 | 0.03 | 0.02 | 0.06 | 0.03 | 0.11 | 0.03 | 0.02 | 0.03 | 0.02 | 0.04 | 0.04 | 0.04 | 0.04 | 0.03 | 0.00 | 0.07 | 0.23 | 0.02 | 0.00 | 0.03 | 0.00 | 0.00 | 0.11 | 0.03 | 0.07 | 0.31 | 0.06 | 0.07 | 0.04 | 0.05 | 0.24 | 0.13 | 0.03 | 0.17 | 0.00 | 0.04 | 0.01 | 0.00 | 0.13 | 0.03 | 0.01 | 0.15 | 0.01 | 0.13 | 0.00 | 0.00 | 0.03 | 0.03 |
| SLC12A4 | ENSG00000124067 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.06 | 0.01 | 0.07 | 0.17 | 0.02 | 0.00 | 0.00 | 0.01 | 0.07 | 0.04 | 0.03 | 0.06 | 0.01 | 0.03 | 0.01 | 0.13 | 0.01 | 0.04 | 0.04 | 0.00 | 0.01 | 0.01 | 0.01 | 0.01 | 0.00 | 0.01 | 0.04 | 0.05 | 0.01 | 0.23 | 0.03 | 0.01 | 0.02 | 0.00 | 0.01 | 0.03 | 0.05 | 0.03 | 0.33 | 0.04 | 0.02 | 0.03 | 0.08 | 0.06 | 0.14 | 0.02 | 0.04 | 0.15 | 0.01 | 0.00 | 0.05 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.03 | 0.05 | 0.01 |
| CACNA2D4 | ENSG00000151062 | 0.02 | 0.00 | 0.00 | 0.01 | 0.04 | 0.00 | 0.02 | 0.06 | 0.13 | 0.03 | 0.01 | 0.00 | 0.04 | 0.01 | 0.10 | 0.06 | 0.22 | 0.01 | 0.15 | 0.01 | 0.18 | 0.03 | 0.13 | 0.06 | 0.13 | 0.01 | 0.17 | 0.03 | 0.13 | 0.04 | 0.04 | 0.03 | 0.30 | 0.05 | 0.05 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.17 | 0.04 | 0.46 | 0.09 | 0.09 | 0.03 | 0.11 | 0.02 | 0.23 | 0.10 | 0.20 | 0.12 | 0.57 | 0.00 | 0.00 | 0.01 | 0.02 | 0.03 | 0.13 | 0.01 | 0.06 | 0.02 | 0.00 | 0.01 | 0.06 | 0.02 |
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