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 |
| PIGF | ENSG00000151665 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.05 | 0.08 | 0.00 | 0.00 | 0.00 | 0.01 | 0.05 | 0.07 | 0.01 | 0.25 | 0.02 | 0.04 | 0.01 | 0.04 | 0.02 | 0.03 | 0.02 | 0.00 | 0.02 | 0.02 | 0.02 | 0.01 | 0.02 | 0.05 | 0.01 | 0.00 | 0.05 | 0.00 | 0.02 | 0.01 | 0.01 | 0.00 | 0.00 | 0.07 | 0.01 | 0.28 | 0.04 | 0.06 | 0.00 | 0.06 | 0.01 | 0.21 | 0.02 | 0.05 | 0.05 | 0.12 | 0.01 | 0.00 | 0.00 | 0.10 | 0.02 | 0.01 | 0.00 | 0.00 | 0.01 | 0.03 | 0.00 | 0.02 | 0.01 |
| MFSD6 | ENSG00000151690 | 0.02 | 0.02 | 0.09 | 0.00 | 0.00 | 0.01 | 0.02 | 0.03 | 0.07 | 0.06 | 0.00 | 0.00 | 0.00 | 0.02 | 0.04 | 0.01 | 0.15 | 0.03 | 0.19 | 0.04 | 0.16 | 0.02 | 0.06 | 0.04 | 0.01 | 0.00 | 0.02 | 0.01 | 0.07 | 0.01 | 0.06 | 0.01 | 0.00 | 0.01 | 0.02 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.08 | 0.02 | 0.44 | 0.04 | 0.13 | 0.02 | 0.08 | 0.01 | 0.01 | 0.03 | 0.07 | 0.09 | 0.06 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.02 |
| KCNJ1 | ENSG00000151704 | 0.00 | 0.02 | 0.00 | 0.05 | 0.00 | 0.03 | 0.02 | 0.05 | 0.04 | 0.11 | 0.00 | 0.00 | 0.11 | 0.06 | 0.07 | 0.10 | 0.05 | 0.13 | 0.04 | 0.14 | 0.10 | 0.13 | 0.05 | 0.07 | 0.01 | 0.01 | 0.01 | 0.02 | 0.02 | 0.02 | 0.01 | 0.09 | 0.00 | 0.23 | 0.02 | 0.10 | 0.00 | 0.05 | 0.00 | 0.00 | 0.03 | 0.21 | 0.25 | 0.19 | 0.05 | 0.31 | 0.05 | 0.08 | 0.09 | 0.22 | 0.03 | 0.27 | 0.00 | 0.28 | 0.04 | 0.00 | 0.13 | 0.00 | 0.05 | 0.01 | 0.01 | 0.01 | 0.00 | 0.10 | 0.01 | 0.28 |
| SLC25A4 | ENSG00000151729 | 0.00 | 0.03 | 0.00 | 0.02 | 0.10 | 0.04 | 0.03 | 0.03 | 0.04 | 0.18 | 0.00 | 0.02 | 0.00 | 0.07 | 0.02 | 0.13 | 0.04 | 0.19 | 0.03 | 0.14 | 0.07 | 0.11 | 0.03 | 0.23 | 0.01 | 0.14 | 0.02 | 0.12 | 0.00 | 0.06 | 0.06 | 0.23 | 0.00 | 0.35 | 0.19 | 0.18 | 0.00 | 0.05 | 0.00 | 0.00 | 0.05 | 0.12 | 0.08 | 0.40 | 0.04 | 0.13 | 0.03 | 0.08 | 0.09 | 0.16 | 0.04 | 0.32 | 0.02 | 0.00 | 0.00 | 0.00 | 0.03 | 0.16 | 0.00 | 0.10 | 0.00 | 0.09 | 0.00 | 0.00 | 0.05 | 0.10 |
| SLC35F4 | ENSG00000151812 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 | 0.03 | 0.04 | 0.00 | 0.01 | 0.00 | 0.03 | 0.08 | 0.02 | 0.04 | 0.04 | 0.05 | 0.01 | 0.05 | 0.01 | 0.04 | 0.03 | 0.00 | 0.02 | 0.02 | 0.02 | 0.03 | 0.00 | 0.02 | 0.06 | 0.05 | 0.10 | 0.02 | 0.05 | 0.01 | 0.01 | 0.00 | 0.00 | 0.06 | 0.05 | 0.04 | 0.21 | 0.01 | 0.02 | 0.01 | 0.02 | 0.00 | 0.06 | 0.03 | 0.09 | 0.00 | 0.01 | 0.00 | 0.00 | 0.04 | 0.00 | 0.01 | 0.06 | 0.01 | 0.05 | 0.03 | 0.00 | 0.01 | 0.03 |
| CCL28 | ENSG00000151882 | 0.00 | 0.00 | 0.00 | 0.01 | 0.03 | 0.00 | 0.02 | 0.02 | 0.13 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.20 | 0.01 | 0.23 | 0.01 | 0.10 | 0.00 | 0.22 | 0.01 | 0.19 | 0.01 | 0.05 | 0.01 | 0.05 | 0.00 | 0.04 | 0.00 | 0.04 | 0.00 | 0.00 | 0.01 | 0.17 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.08 | 0.02 | 0.22 | 0.02 | 0.07 | 0.00 | 0.08 | 0.01 | 0.25 | 0.03 | 0.22 | 0.02 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 | 0.00 | 0.00 | 0.01 | 0.00 | 0.02 | 0.00 | 0.00 | 0.11 | 0.02 |
| TUBA3E | ENSG00000152086 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.15 | 0.05 | 0.03 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.01 | 0.08 | 0.02 | 0.05 | 0.01 | 0.08 | 0.06 | 0.03 | 0.05 | 0.01 | 0.01 | 0.00 | 0.01 | 0.02 | 0.01 | 0.02 | 0.03 | 0.00 | 0.03 | 0.05 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.05 | 0.08 | 0.18 | 0.02 | 0.00 | 0.04 | 0.01 | 0.07 | 0.00 | 0.15 | 0.03 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.12 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 |
| CYSLTR2 | ENSG00000152207 | 0.02 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.39 | 0.05 | 0.32 | 0.00 | 0.00 | 0.00 | 0.14 | 0.01 | 0.07 | 0.01 | 0.12 | 0.02 | 0.14 | 0.04 | 0.09 | 0.12 | 0.04 | 0.10 | 0.03 | 0.10 | 0.04 | 0.01 | 0.03 | 0.00 | 0.30 | 0.00 | 0.09 | 0.00 | 0.03 | 0.01 | 0.00 | 0.00 | 0.02 | 0.01 | 0.14 | 0.03 | 0.28 | 0.00 | 0.21 | 0.01 | 0.05 | 0.03 | 0.22 | 0.01 | 0.61 | 0.00 | 0.02 | 0.00 | 0.00 | 0.03 | 0.12 | 0.01 | 0.08 | 0.00 | 0.17 | 0.00 | 0.00 | 0.01 | 0.04 |
| SUV39H2 | ENSG00000152455 | 0.01 | 0.01 | 0.03 | 0.00 | 0.00 | 0.00 | 0.01 | 0.03 | 0.14 | 0.03 | 0.00 | 0.00 | 0.03 | 0.08 | 0.03 | 0.04 | 0.02 | 0.06 | 0.02 | 0.03 | 0.06 | 0.03 | 0.06 | 0.03 | 0.01 | 0.01 | 0.00 | 0.00 | 0.03 | 0.02 | 0.00 | 0.01 | 0.00 | 0.05 | 0.06 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.12 | 0.01 | 0.17 | 0.06 | 0.02 | 0.01 | 0.04 | 0.02 | 0.29 | 0.00 | 0.05 | 0.06 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.00 | 0.03 | 0.01 | 0.02 | 0.01 | 0.00 | 0.02 | 0.03 | 0.01 |
| TMEM123 | ENSG00000152558 | 0.03 | 0.00 | 0.00 | 0.05 | 0.03 | 0.03 | 0.02 | 0.05 | 0.29 | 0.05 | 0.00 | 0.00 | 0.08 | 0.06 | 0.11 | 0.04 | 0.11 | 0.07 | 0.44 | 0.09 | 0.14 | 0.08 | 0.10 | 0.05 | 0.04 | 0.01 | 0.02 | 0.02 | 0.02 | 0.01 | 0.05 | 0.06 | 0.00 | 0.10 | 0.01 | 0.05 | 0.00 | 0.04 | 0.00 | 0.00 | 0.06 | 0.18 | 0.36 | 0.12 | 0.86 | 0.10 | 0.10 | 0.04 | 0.11 | 0.17 | 0.30 | 0.11 | 0.02 | 0.08 | 0.02 | 0.00 | 0.04 | 0.01 | 0.01 | 0.01 | 0.00 | 0.01 | 0.03 | 0.00 | 0.19 | 0.12 |
| GRIA4 | ENSG00000152578 | 0.00 | 0.01 | 0.00 | 0.06 | 0.01 | 0.03 | 0.02 | 0.08 | 0.07 | 0.10 | 0.00 | 0.00 | 0.02 | 0.11 | 0.07 | 0.07 | 0.07 | 0.08 | 0.06 | 0.14 | 0.09 | 0.10 | 0.02 | 0.06 | 0.02 | 0.02 | 0.02 | 0.04 | 0.01 | 0.02 | 0.01 | 0.07 | 0.00 | 0.14 | 0.00 | 0.07 | 0.01 | 0.06 | 0.00 | 0.00 | 0.05 | 0.21 | 0.24 | 0.15 | 0.11 | 0.24 | 0.02 | 0.05 | 0.14 | 0.27 | 0.11 | 0.19 | 0.01 | 0.10 | 0.02 | 0.00 | 0.07 | 0.01 | 0.01 | 0.01 | 0.00 | 0.02 | 0.00 | 0.01 | 0.06 | 0.20 |
| DSPP | ENSG00000152591 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.03 | 0.03 | 0.13 | 0.05 | 0.00 | 0.00 | 0.00 | 0.06 | 0.02 | 0.03 | 0.07 | 0.04 | 0.05 | 0.02 | 0.04 | 0.07 | 0.03 | 0.07 | 0.01 | 0.02 | 0.00 | 0.01 | 0.00 | 0.01 | 0.02 | 0.11 | 0.00 | 0.03 | 0.09 | 0.02 | 0.02 | 0.02 | 0.00 | 0.00 | 0.04 | 0.04 | 0.05 | 0.22 | 0.01 | 0.03 | 0.02 | 0.02 | 0.02 | 0.09 | 0.05 | 0.07 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.05 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.05 |
| DMP1 | ENSG00000152592 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.03 | 0.03 | 0.13 | 0.05 | 0.00 | 0.00 | 0.00 | 0.06 | 0.02 | 0.03 | 0.07 | 0.04 | 0.05 | 0.02 | 0.04 | 0.07 | 0.03 | 0.07 | 0.01 | 0.02 | 0.00 | 0.01 | 0.00 | 0.01 | 0.02 | 0.11 | 0.00 | 0.03 | 0.09 | 0.02 | 0.02 | 0.02 | 0.00 | 0.00 | 0.03 | 0.04 | 0.05 | 0.22 | 0.01 | 0.03 | 0.02 | 0.02 | 0.02 | 0.09 | 0.05 | 0.07 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.05 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.05 |
| MEPE | ENSG00000152595 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.03 | 0.03 | 0.12 | 0.05 | 0.00 | 0.00 | 0.00 | 0.07 | 0.02 | 0.03 | 0.07 | 0.04 | 0.04 | 0.02 | 0.04 | 0.07 | 0.03 | 0.06 | 0.01 | 0.02 | 0.00 | 0.01 | 0.00 | 0.01 | 0.02 | 0.11 | 0.00 | 0.03 | 0.09 | 0.02 | 0.02 | 0.02 | 0.00 | 0.00 | 0.03 | 0.04 | 0.04 | 0.22 | 0.01 | 0.03 | 0.02 | 0.02 | 0.02 | 0.09 | 0.05 | 0.07 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.05 | 0.00 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.05 |
| PELO | ENSG00000152684 | 0.00 | 0.00 | 0.00 | 0.01 | 0.03 | 0.00 | 0.01 | 0.14 | 0.06 | 0.11 | 0.00 | 0.00 | 0.01 | 0.01 | 0.05 | 0.06 | 0.05 | 0.09 | 0.02 | 0.08 | 0.04 | 0.14 | 0.02 | 0.09 | 0.03 | 0.04 | 0.02 | 0.03 | 0.00 | 0.05 | 0.02 | 0.01 | 0.00 | 0.10 | 0.09 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.03 | 0.08 | 0.10 | 0.38 | 0.04 | 0.08 | 0.03 | 0.11 | 0.04 | 0.26 | 0.07 | 0.05 | 0.00 | 0.02 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.03 | 0.02 |
| CNTNAP4 | ENSG00000152910 | 0.00 | 0.00 | 0.01 | 0.03 | 0.00 | 0.06 | 0.00 | 0.22 | 0.12 | 0.04 | 0.00 | 0.00 | 0.00 | 0.12 | 0.03 | 0.07 | 0.05 | 0.05 | 0.02 | 0.03 | 0.05 | 0.04 | 0.03 | 0.03 | 0.01 | 0.01 | 0.03 | 0.02 | 0.01 | 0.01 | 0.00 | 0.05 | 0.05 | 0.01 | 0.06 | 0.09 | 0.00 | 0.02 | 0.00 | 0.01 | 0.04 | 0.06 | 0.04 | 0.29 | 0.04 | 0.04 | 0.02 | 0.08 | 0.04 | 0.26 | 0.03 | 0.06 | 0.00 | 0.09 | 0.00 | 0.05 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.05 | 0.00 | 0.02 | 0.01 | 0.05 |
| MR1 | ENSG00000153029 | 0.02 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.02 | 0.23 | 0.02 | 0.02 | 0.00 | 0.09 | 0.03 | 0.11 | 0.00 | 0.16 | 0.02 | 0.03 | 0.00 | 0.14 | 0.02 | 0.10 | 0.01 | 0.03 | 0.00 | 0.12 | 0.00 | 0.04 | 0.00 | 0.15 | 0.01 | 0.17 | 0.01 | 0.02 | 0.04 | 0.02 | 0.00 | 0.00 | 0.00 | 0.17 | 0.01 | 0.36 | 0.03 | 0.08 | 0.01 | 0.08 | 0.00 | 0.29 | 0.00 | 0.23 | 0.04 | 0.07 | 0.00 | 0.01 | 0.00 | 0.32 | 0.00 | 0.01 | 0.00 | 0.02 | 0.01 | 0.02 | 0.00 | 0.12 | 0.02 |
| OR14K1 | ENSG00000153230 | 0.01 | 0.02 | 0.01 | 0.01 | 0.00 | 0.01 | 0.02 | 0.04 | 0.14 | 0.04 | 0.02 | 0.02 | 0.08 | 0.05 | 0.13 | 0.01 | 0.17 | 0.03 | 0.10 | 0.02 | 0.27 | 0.04 | 0.13 | 0.01 | 0.04 | 0.02 | 0.08 | 0.01 | 0.02 | 0.01 | 0.20 | 0.02 | 0.23 | 0.02 | 0.10 | 0.07 | 0.00 | 0.04 | 0.00 | 0.00 | 0.29 | 0.02 | 0.48 | 0.12 | 0.13 | 0.01 | 0.12 | 0.02 | 0.32 | 0.00 | 0.09 | 0.24 | 0.06 | 0.02 | 0.01 | 0.00 | 0.03 | 0.18 | 0.02 | 0.04 | 0.02 | 0.04 | 0.15 | 0.03 | 0.24 | 0.02 |
| CD8A | ENSG00000153563 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.03 | 0.07 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.02 | 0.02 | 0.10 | 0.01 | 0.06 | 0.01 | 0.11 | 0.01 | 0.04 | 0.01 | 0.00 | 0.01 | 0.01 | 0.02 | 0.00 | 0.01 | 0.02 | 0.02 | 0.00 | 0.02 | 0.04 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.04 | 0.02 | 0.11 | 0.05 | 0.05 | 0.01 | 0.03 | 0.02 | 0.09 | 0.03 | 0.21 | 0.04 | 0.01 | 0.04 | 0.00 | 0.00 | 0.04 | 0.04 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 |
| KCNJ16 | ENSG00000153822 | 0.02 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.03 | 0.02 | 0.24 | 0.01 | 0.02 | 0.00 | 0.13 | 0.00 | 0.17 | 0.00 | 0.21 | 0.01 | 0.07 | 0.02 | 0.26 | 0.03 | 0.11 | 0.03 | 0.07 | 0.01 | 0.06 | 0.05 | 0.05 | 0.10 | 0.22 | 0.01 | 0.12 | 0.01 | 0.14 | 0.09 | 0.02 | 0.01 | 0.00 | 0.00 | 0.42 | 0.02 | 0.26 | 0.03 | 0.14 | 0.03 | 0.11 | 0.02 | 0.34 | 0.02 | 0.23 | 0.03 | 0.02 | 0.00 | 0.00 | 0.00 | 0.05 | 0.00 | 0.08 | 0.00 | 0.03 | 0.01 | 0.17 | 0.01 | 0.23 | 0.01 |
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