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 |
| FNDC5 | ENSG00000160097 | 0.00 | 0.04 | 0.00 | 0.05 | 0.00 | 0.00 | 0.02 | 0.01 | 0.03 | 0.07 | 0.00 | 0.01 | 0.11 | 0.07 | 0.06 | 0.04 | 0.05 | 0.05 | 0.06 | 0.04 | 0.06 | 0.05 | 0.07 | 0.05 | 0.02 | 0.08 | 0.01 | 0.11 | 0.01 | 0.03 | 0.03 | 0.17 | 0.00 | 0.61 | 0.04 | 0.05 | 0.02 | 0.08 | 0.00 | 0.00 | 0.05 | 0.09 | 0.35 | 0.21 | 0.06 | 0.03 | 0.06 | 0.06 | 0.09 | 0.04 | 0.14 | 0.05 | 0.03 | 0.03 | 0.02 | 0.00 | 0.00 | 0.07 | 0.00 | 0.01 | 0.05 | 0.04 | 0.00 | 0.07 | 0.05 | 0.05 |
| CILP2 | ENSG00000160161 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.05 | 0.03 | 0.01 | 0.03 | 0.05 | 0.00 | 0.04 | 0.03 | 0.12 | 0.02 | 0.05 | 0.02 | 0.17 | 0.02 | 0.05 | 0.01 | 0.00 | 0.00 | 0.03 | 0.04 | 0.01 | 0.02 | 0.07 | 0.02 | 0.00 | 0.03 | 0.14 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.08 | 0.02 | 0.43 | 0.07 | 0.02 | 0.02 | 0.14 | 0.04 | 0.25 | 0.09 | 0.06 | 0.04 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.06 | 0.01 | 0.00 | 0.01 | 0.01 | 0.02 | 0.00 | 0.04 | 0.01 |
| TFF3 | ENSG00000160180 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.05 | 0.05 | 0.04 | 0.00 | 0.03 | 0.00 | 0.00 | 0.02 | 0.02 | 0.02 | 0.07 | 0.01 | 0.05 | 0.02 | 0.09 | 0.04 | 0.07 | 0.01 | 0.01 | 0.01 | 0.05 | 0.01 | 0.01 | 0.02 | 0.02 | 0.07 | 0.03 | 0.01 | 0.04 | 0.01 | 0.00 | 0.00 | 0.00 | 0.08 | 0.02 | 0.13 | 0.16 | 0.04 | 0.04 | 0.04 | 0.02 | 0.19 | 0.03 | 0.09 | 0.06 | 0.04 | 0.00 | 0.12 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.03 | 0.00 | 0.01 | 0.02 |
| TFF2 | ENSG00000160181 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.05 | 0.05 | 0.04 | 0.00 | 0.03 | 0.00 | 0.00 | 0.02 | 0.02 | 0.02 | 0.07 | 0.01 | 0.05 | 0.02 | 0.09 | 0.04 | 0.07 | 0.01 | 0.01 | 0.02 | 0.05 | 0.01 | 0.01 | 0.02 | 0.02 | 0.07 | 0.03 | 0.01 | 0.04 | 0.01 | 0.00 | 0.00 | 0.00 | 0.08 | 0.02 | 0.13 | 0.16 | 0.04 | 0.04 | 0.04 | 0.02 | 0.19 | 0.03 | 0.09 | 0.07 | 0.04 | 0.00 | 0.12 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.03 | 0.00 | 0.01 | 0.02 |
| TFF1 | ENSG00000160182 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.05 | 0.05 | 0.04 | 0.00 | 0.03 | 0.00 | 0.00 | 0.02 | 0.02 | 0.02 | 0.07 | 0.01 | 0.05 | 0.04 | 0.09 | 0.04 | 0.07 | 0.01 | 0.01 | 0.02 | 0.05 | 0.01 | 0.01 | 0.02 | 0.02 | 0.05 | 0.07 | 0.01 | 0.04 | 0.01 | 0.00 | 0.00 | 0.00 | 0.09 | 0.02 | 0.13 | 0.16 | 0.04 | 0.04 | 0.04 | 0.02 | 0.19 | 0.03 | 0.06 | 0.07 | 0.04 | 0.00 | 0.12 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.03 | 0.00 | 0.01 | 0.02 |
| TMPRSS3 | ENSG00000160183 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.05 | 0.05 | 0.05 | 0.00 | 0.03 | 0.00 | 0.00 | 0.03 | 0.02 | 0.02 | 0.07 | 0.01 | 0.05 | 0.04 | 0.09 | 0.04 | 0.07 | 0.01 | 0.01 | 0.02 | 0.05 | 0.01 | 0.01 | 0.02 | 0.02 | 0.05 | 0.07 | 0.01 | 0.04 | 0.01 | 0.00 | 0.00 | 0.00 | 0.08 | 0.02 | 0.13 | 0.16 | 0.04 | 0.04 | 0.04 | 0.02 | 0.19 | 0.03 | 0.06 | 0.07 | 0.04 | 0.00 | 0.12 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 | 0.03 | 0.00 | 0.01 | 0.03 |
| PDXK | ENSG00000160209 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.03 | 0.06 | 0.05 | 0.00 | 0.03 | 0.00 | 0.03 | 0.03 | 0.02 | 0.03 | 0.06 | 0.02 | 0.05 | 0.03 | 0.08 | 0.03 | 0.07 | 0.01 | 0.02 | 0.01 | 0.08 | 0.01 | 0.01 | 0.02 | 0.02 | 0.05 | 0.07 | 0.13 | 0.04 | 0.01 | 0.00 | 0.00 | 0.00 | 0.09 | 0.02 | 0.19 | 0.18 | 0.04 | 0.02 | 0.07 | 0.02 | 0.33 | 0.03 | 0.08 | 0.08 | 0.04 | 0.00 | 0.13 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.02 | 0.01 | 0.06 | 0.00 | 0.02 | 0.03 |
| CSTB | ENSG00000160213 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.03 | 0.06 | 0.05 | 0.00 | 0.02 | 0.00 | 0.03 | 0.02 | 0.02 | 0.03 | 0.06 | 0.02 | 0.05 | 0.03 | 0.08 | 0.03 | 0.07 | 0.01 | 0.02 | 0.01 | 0.07 | 0.01 | 0.01 | 0.02 | 0.02 | 0.05 | 0.07 | 0.13 | 0.04 | 0.01 | 0.00 | 0.00 | 0.00 | 0.09 | 0.02 | 0.20 | 0.18 | 0.04 | 0.02 | 0.07 | 0.02 | 0.33 | 0.03 | 0.08 | 0.08 | 0.04 | 0.00 | 0.12 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.02 | 0.01 | 0.06 | 0.00 | 0.02 | 0.03 |
| AIRE | ENSG00000160224 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.04 | 0.05 | 0.04 | 0.00 | 0.02 | 0.00 | 0.01 | 0.03 | 0.02 | 0.03 | 0.06 | 0.02 | 0.06 | 0.05 | 0.08 | 0.02 | 0.06 | 0.01 | 0.03 | 0.01 | 0.06 | 0.01 | 0.01 | 0.03 | 0.02 | 0.05 | 0.07 | 0.09 | 0.04 | 0.01 | 0.00 | 0.00 | 0.00 | 0.10 | 0.02 | 0.21 | 0.18 | 0.05 | 0.03 | 0.06 | 0.02 | 0.10 | 0.08 | 0.08 | 0.09 | 0.04 | 0.00 | 0.10 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.02 | 0.06 | 0.00 | 0.02 | 0.03 |
| S100B | ENSG00000160307 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.03 | 0.07 | 0.04 | 0.00 | 0.02 | 0.02 | 0.01 | 0.06 | 0.02 | 0.06 | 0.07 | 0.03 | 0.07 | 0.07 | 0.06 | 0.02 | 0.06 | 0.01 | 0.02 | 0.01 | 0.09 | 0.02 | 0.01 | 0.04 | 0.03 | 0.05 | 0.07 | 0.01 | 0.08 | 0.01 | 0.00 | 0.00 | 0.00 | 0.12 | 0.02 | 0.21 | 0.18 | 0.05 | 0.03 | 0.04 | 0.03 | 0.06 | 0.16 | 0.12 | 0.18 | 0.04 | 0.01 | 0.10 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.02 | 0.03 | 0.00 | 0.02 | 0.04 |
| SLC2A6 | ENSG00000160326 | 0.00 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.04 | 0.01 | 0.05 | 0.02 | 0.00 | 0.01 | 0.00 | 0.02 | 0.05 | 0.02 | 0.07 | 0.03 | 0.07 | 0.03 | 0.12 | 0.04 | 0.12 | 0.01 | 0.02 | 0.01 | 0.05 | 0.03 | 0.01 | 0.00 | 0.05 | 0.03 | 0.06 | 0.01 | 0.12 | 0.04 | 0.00 | 0.01 | 0.00 | 0.00 | 0.05 | 0.06 | 0.07 | 0.25 | 0.07 | 0.01 | 0.02 | 0.06 | 0.04 | 0.14 | 0.07 | 0.14 | 0.03 | 0.03 | 0.01 | 0.00 | 0.05 | 0.00 | 0.02 | 0.01 | 0.03 | 0.03 | 0.00 | 0.00 | 0.02 | 0.02 |
| FCN2 | ENSG00000160339 | 0.00 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.04 | 0.01 | 0.03 | 0.03 | 0.00 | 0.01 | 0.00 | 0.02 | 0.05 | 0.03 | 0.07 | 0.02 | 0.07 | 0.03 | 0.12 | 0.02 | 0.11 | 0.02 | 0.03 | 0.01 | 0.07 | 0.04 | 0.01 | 0.00 | 0.06 | 0.04 | 0.06 | 0.01 | 0.19 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.05 | 0.07 | 0.08 | 0.25 | 0.06 | 0.02 | 0.02 | 0.05 | 0.03 | 0.14 | 0.07 | 0.15 | 0.03 | 0.03 | 0.01 | 0.01 | 0.05 | 0.00 | 0.02 | 0.01 | 0.03 | 0.03 | 0.00 | 0.00 | 0.03 | 0.02 |
| LCN1 | ENSG00000160349 | 0.00 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.02 | 0.01 | 0.03 | 0.04 | 0.00 | 0.00 | 0.00 | 0.02 | 0.06 | 0.03 | 0.07 | 0.02 | 0.07 | 0.03 | 0.13 | 0.02 | 0.11 | 0.02 | 0.03 | 0.01 | 0.08 | 0.04 | 0.01 | 0.00 | 0.06 | 0.04 | 0.06 | 0.01 | 0.12 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.05 | 0.06 | 0.13 | 0.24 | 0.06 | 0.02 | 0.01 | 0.05 | 0.03 | 0.20 | 0.07 | 0.16 | 0.03 | 0.03 | 0.01 | 0.00 | 0.05 | 0.00 | 0.02 | 0.01 | 0.03 | 0.02 | 0.00 | 0.00 | 0.03 | 0.02 |
| HIPK4 | ENSG00000160396 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.02 | 0.01 | 0.03 | 0.21 | 0.02 | 0.00 | 0.00 | 0.08 | 0.02 | 0.17 | 0.04 | 0.45 | 0.06 | 0.06 | 0.02 | 0.04 | 0.05 | 0.07 | 0.02 | 0.07 | 0.01 | 0.01 | 0.01 | 0.24 | 0.01 | 0.07 | 0.02 | 0.12 | 0.01 | 0.17 | 0.03 | 0.00 | 0.02 | 0.00 | 0.00 | 0.12 | 0.03 | 0.44 | 0.21 | 0.14 | 0.04 | 0.19 | 0.03 | 0.91 | 0.11 | 0.25 | 0.11 | 0.00 | 0.03 | 0.01 | 0.00 | 0.05 | 0.00 | 0.02 | 0.06 | 0.03 | 0.06 | 0.00 | 0.00 | 0.03 | 0.01 |
| TOR2A | ENSG00000160404 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.05 | 0.00 | 0.03 | 0.02 | 0.00 | 0.01 | 0.00 | 0.02 | 0.04 | 0.02 | 0.06 | 0.02 | 0.06 | 0.01 | 0.12 | 0.02 | 0.10 | 0.01 | 0.01 | 0.01 | 0.04 | 0.02 | 0.00 | 0.01 | 0.04 | 0.03 | 0.07 | 0.04 | 0.08 | 0.04 | 0.01 | 0.00 | 0.00 | 0.00 | 0.09 | 0.03 | 0.10 | 0.17 | 0.05 | 0.01 | 0.08 | 0.03 | 0.15 | 0.11 | 0.04 | 0.07 | 0.02 | 0.04 | 0.01 | 0.00 | 0.05 | 0.00 | 0.02 | 0.00 | 0.03 | 0.01 | 0.00 | 0.00 | 0.05 | 0.02 |
| MPZL3 | ENSG00000160588 | 0.02 | 0.01 | 0.00 | 0.06 | 0.02 | 0.02 | 0.02 | 0.08 | 0.04 | 0.11 | 0.00 | 0.00 | 0.07 | 0.06 | 0.05 | 0.07 | 0.05 | 0.09 | 0.04 | 0.15 | 0.04 | 0.11 | 0.07 | 0.07 | 0.01 | 0.01 | 0.03 | 0.03 | 0.01 | 0.02 | 0.02 | 0.09 | 0.00 | 0.17 | 0.03 | 0.05 | 0.00 | 0.06 | 0.00 | 0.00 | 0.03 | 0.23 | 0.14 | 0.14 | 0.05 | 0.30 | 0.05 | 0.04 | 0.15 | 0.16 | 0.04 | 0.21 | 0.00 | 0.15 | 0.02 | 0.00 | 0.14 | 0.01 | 0.07 | 0.01 | 0.01 | 0.01 | 0.00 | 0.07 | 0.01 | 0.26 |
| PCSK7 | ENSG00000160613 | 0.00 | 0.01 | 0.00 | 0.06 | 0.02 | 0.02 | 0.01 | 0.09 | 0.03 | 0.11 | 0.00 | 0.00 | 0.02 | 0.05 | 0.05 | 0.08 | 0.04 | 0.09 | 0.03 | 0.16 | 0.04 | 0.12 | 0.06 | 0.08 | 0.01 | 0.02 | 0.00 | 0.03 | 0.01 | 0.01 | 0.01 | 0.09 | 0.00 | 0.17 | 0.00 | 0.05 | 0.00 | 0.06 | 0.00 | 0.00 | 0.02 | 0.24 | 0.15 | 0.16 | 0.04 | 0.29 | 0.04 | 0.05 | 0.12 | 0.20 | 0.03 | 0.23 | 0.00 | 0.15 | 0.02 | 0.00 | 0.11 | 0.01 | 0.04 | 0.01 | 0.01 | 0.01 | 0.00 | 0.07 | 0.00 | 0.27 |
| CXCR5 | ENSG00000160683 | 0.01 | 0.01 | 0.02 | 0.06 | 0.02 | 0.02 | 0.02 | 0.08 | 0.04 | 0.11 | 0.00 | 0.00 | 0.11 | 0.04 | 0.05 | 0.07 | 0.05 | 0.09 | 0.04 | 0.16 | 0.04 | 0.12 | 0.06 | 0.07 | 0.01 | 0.01 | 0.03 | 0.03 | 0.01 | 0.02 | 0.02 | 0.09 | 0.00 | 0.17 | 0.10 | 0.05 | 0.00 | 0.06 | 0.00 | 0.00 | 0.03 | 0.21 | 0.16 | 0.14 | 0.04 | 0.30 | 0.07 | 0.05 | 0.22 | 0.11 | 0.04 | 0.22 | 0.00 | 0.15 | 0.03 | 0.01 | 0.14 | 0.01 | 0.06 | 0.01 | 0.03 | 0.01 | 0.00 | 0.07 | 0.01 | 0.25 |
| IL6R | ENSG00000160712 | 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 | 0.24 | 0.00 | 0.17 | 0.01 | 0.03 | 0.00 | 0.11 | 0.00 | 0.07 | 0.00 | 0.36 | 0.00 | 0.49 | 0.01 | 0.21 | 0.00 | 0.10 | 0.00 | 0.00 | 0.00 | 0.32 | 0.00 | 0.49 | 0.02 | 0.19 | 0.00 | 0.19 | 0.00 | 0.50 | 0.00 | 0.41 | 0.01 | 0.11 | 0.00 | 0.00 | 0.00 | 0.25 | 0.00 | 0.02 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.22 | 0.00 |
| CHRNB2 | ENSG00000160716 | 0.03 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.07 | 0.00 | 0.37 | 0.01 | 0.02 | 0.00 | 0.11 | 0.00 | 0.37 | 0.00 | 0.26 | 0.00 | 0.05 | 0.00 | 0.22 | 0.00 | 0.18 | 0.00 | 0.03 | 0.00 | 0.11 | 0.00 | 0.09 | 0.00 | 0.35 | 0.00 | 0.49 | 0.01 | 0.21 | 0.00 | 0.10 | 0.00 | 0.00 | 0.00 | 0.31 | 0.00 | 0.48 | 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 |
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