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 |
| TNFRSF11B | ENSG00000164761 | 0.02 | 0.00 | 0.01 | 0.00 | 0.09 | 0.00 | 0.06 | 0.01 | 0.25 | 0.02 | 0.02 | 0.01 | 0.02 | 0.03 | 0.22 | 0.01 | 0.33 | 0.01 | 0.24 | 0.00 | 0.47 | 0.01 | 0.27 | 0.00 | 0.15 | 0.00 | 0.26 | 0.00 | 0.14 | 0.00 | 0.38 | 0.01 | 0.25 | 0.01 | 0.04 | 0.00 | 0.02 | 0.01 | 0.00 | 0.00 | 0.54 | 0.02 | 1.23 | 0.05 | 0.16 | 0.00 | 0.15 | 0.01 | 0.32 | 0.00 | 0.17 | 0.05 | 0.05 | 0.02 | 0.02 | 0.00 | 0.21 | 0.00 | 0.19 | 0.00 | 0.02 | 0.01 | 0.53 | 0.00 | 0.17 | 0.01 |
| INHA | ENSG00000123999 | 0.01 | 0.07 | 0.04 | 0.04 | 0.00 | 0.03 | 0.01 | 0.03 | 0.01 | 0.27 | 0.00 | 0.02 | 0.00 | 0.10 | 0.02 | 0.03 | 0.04 | 0.19 | 0.00 | 0.18 | 0.04 | 0.13 | 0.05 | 0.04 | 0.02 | 0.01 | 0.02 | 0.02 | 0.05 | 0.03 | 0.03 | 0.04 | 0.00 | 0.04 | 0.03 | 0.03 | 0.01 | 0.00 | 0.00 | 0.01 | 0.04 | 0.06 | 0.18 | 0.16 | 0.03 | 0.34 | 0.04 | 0.04 | 0.08 | 0.05 | 0.08 | 0.20 | 0.08 | 0.01 | 0.00 | 0.00 | 0.00 | 0.04 | 0.00 | 0.02 | 0.00 | 0.00 | 0.02 | 0.02 | 0.02 | 0.04 |
| PKDCC | ENSG00000162878 | 0.00 | 0.01 | 0.02 | 0.01 | 0.00 | 0.00 | 0.01 | 0.08 | 0.06 | 0.01 | 0.00 | 0.00 | 0.01 | 0.07 | 0.05 | 0.01 | 0.12 | 0.02 | 0.03 | 0.01 | 0.07 | 0.03 | 0.04 | 0.03 | 0.00 | 0.02 | 0.00 | 0.03 | 0.01 | 0.02 | 0.08 | 0.01 | 0.00 | 0.05 | 0.05 | 0.03 | 0.02 | 0.01 | 0.00 | 0.00 | 0.05 | 0.02 | 0.24 | 0.05 | 0.08 | 0.00 | 0.09 | 0.02 | 0.22 | 0.00 | 0.05 | 0.06 | 0.17 | 0.01 | 0.00 | 0.00 | 0.10 | 0.02 | 0.01 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.01 | 0.01 |
| GGT6 | ENSG00000167741 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.09 | 0.05 | 0.03 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.05 | 0.02 | 0.03 | 0.02 | 0.03 | 0.06 | 0.04 | 0.03 | 0.02 | 0.01 | 0.01 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.13 | 0.00 | 0.03 | 0.02 | 0.04 | 0.00 | 0.03 | 0.00 | 0.00 | 0.03 | 0.05 | 0.11 | 0.07 | 0.01 | 0.03 | 0.04 | 0.04 | 0.05 | 0.12 | 0.16 | 0.24 | 0.00 | 0.02 | 0.00 | 0.02 | 0.00 | 0.06 | 0.00 | 0.00 | 0.00 | 0.06 | 0.00 | 0.00 | 0.05 | 0.03 |
| MAP2K4 | ENSG00000065559 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.08 | 0.03 | 0.10 | 0.00 | 0.01 | 0.00 | 0.05 | 0.00 | 0.06 | 0.02 | 0.02 | 0.02 | 0.02 | 0.03 | 0.11 | 0.00 | 0.10 | 0.00 | 0.08 | 0.00 | 0.07 | 0.00 | 0.08 | 0.01 | 0.10 | 0.03 | 0.04 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.13 | 0.01 | 0.20 | 0.00 | 0.07 | 0.02 | 0.07 | 0.06 | 0.22 | 0.67 | 0.06 | 0.01 | 0.02 | 0.00 | 0.00 | 0.04 | 0.02 | 0.00 | 0.00 | 0.02 | 0.03 | 0.00 | 0.00 | 0.02 | 0.02 |
| EPHA1 | ENSG00000146904 | 0.02 | 0.01 | 0.05 | 0.00 | 0.05 | 0.02 | 0.02 | 0.03 | 0.05 | 0.03 | 0.00 | 0.01 | 0.04 | 0.05 | 0.07 | 0.02 | 0.08 | 0.07 | 0.02 | 0.15 | 0.03 | 0.20 | 0.02 | 0.10 | 0.03 | 0.00 | 0.02 | 0.03 | 0.02 | 0.05 | 0.04 | 0.05 | 0.00 | 0.11 | 0.06 | 0.06 | 0.00 | 0.02 | 0.00 | 0.00 | 0.08 | 0.05 | 0.55 | 0.05 | 0.03 | 0.09 | 0.05 | 0.05 | 0.10 | 0.14 | 0.13 | 0.11 | 0.02 | 0.04 | 0.00 | 0.05 | 0.02 | 0.09 | 0.11 | 0.01 | 0.04 | 0.02 | 0.00 | 0.03 | 0.21 | 0.02 |
| PTPRM | ENSG00000173482 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.02 | 0.01 | 0.07 | 0.04 | 0.02 | 0.00 | 0.00 | 0.00 | 0.05 | 0.03 | 0.04 | 0.01 | 0.05 | 0.02 | 0.11 | 0.09 | 0.08 | 0.04 | 0.02 | 0.04 | 0.04 | 0.03 | 0.04 | 0.02 | 0.01 | 0.02 | 0.00 | 0.09 | 0.00 | 0.06 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.04 | 0.08 | 0.09 | 0.06 | 0.04 | 0.04 | 0.01 | 0.06 | 0.02 | 0.13 | 0.04 | 0.03 | 0.04 | 0.00 | 0.01 | 0.00 | 0.04 | 0.01 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.02 | 0.02 |
| KCNK7 | ENSG00000173338 | 0.01 | 0.00 | 0.00 | 0.01 | 0.07 | 0.00 | 0.08 | 0.01 | 0.20 | 0.01 | 0.00 | 0.00 | 0.08 | 0.00 | 0.09 | 0.03 | 0.09 | 0.02 | 0.30 | 0.02 | 0.18 | 0.04 | 0.07 | 0.03 | 0.01 | 0.02 | 0.02 | 0.04 | 0.00 | 0.03 | 0.02 | 0.04 | 0.00 | 0.11 | 0.07 | 0.07 | 0.03 | 0.01 | 0.00 | 0.00 | 0.14 | 0.09 | 0.23 | 0.04 | 0.13 | 0.01 | 0.07 | 0.03 | 0.20 | 0.06 | 0.13 | 0.03 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.01 | 0.01 | 0.03 | 0.00 | 0.00 | 0.08 | 0.06 |
| TCN1 | ENSG00000134827 | 0.01 | 0.00 | 0.00 | 0.01 | 0.09 | 0.00 | 0.02 | 0.01 | 0.15 | 0.02 | 0.00 | 0.00 | 0.09 | 0.01 | 0.04 | 0.02 | 0.07 | 0.03 | 0.11 | 0.03 | 0.09 | 0.04 | 0.02 | 0.04 | 0.01 | 0.01 | 0.03 | 0.02 | 0.00 | 0.02 | 0.02 | 0.03 | 0.04 | 0.07 | 0.06 | 0.00 | 0.02 | 0.01 | 0.00 | 0.00 | 0.10 | 0.08 | 0.11 | 0.05 | 0.05 | 0.03 | 0.06 | 0.01 | 0.16 | 0.13 | 0.04 | 0.04 | 0.00 | 0.05 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.07 | 0.04 |
| BAZ2B | ENSG00000123636 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.10 | 0.11 | 0.06 | 0.00 | 0.01 | 0.00 | 0.00 | 0.04 | 0.01 | 0.10 | 0.03 | 0.04 | 0.03 | 0.10 | 0.04 | 0.03 | 0.05 | 0.01 | 0.02 | 0.01 | 0.01 | 0.05 | 0.01 | 0.05 | 0.06 | 0.00 | 0.05 | 0.02 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.04 | 0.34 | 0.05 | 0.05 | 0.02 | 0.07 | 0.01 | 0.06 | 0.04 | 0.05 | 0.10 | 0.03 | 0.01 | 0.00 | 0.00 | 0.00 | 0.15 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.03 | 0.01 |
| F2R | ENSG00000181104 | 0.00 | 0.01 | 0.01 | 0.01 | 0.03 | 0.01 | 0.00 | 0.17 | 0.02 | 0.12 | 0.00 | 0.01 | 0.00 | 0.03 | 0.01 | 0.07 | 0.00 | 0.10 | 0.01 | 0.07 | 0.02 | 0.15 | 0.02 | 0.12 | 0.00 | 0.06 | 0.01 | 0.05 | 0.00 | 0.07 | 0.02 | 0.03 | 0.00 | 0.13 | 0.09 | 0.00 | 0.00 | 0.03 | 0.00 | 0.00 | 0.01 | 0.09 | 0.04 | 0.70 | 0.00 | 0.05 | 0.01 | 0.10 | 0.00 | 0.23 | 0.04 | 0.05 | 0.00 | 0.01 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.05 | 0.04 |
| SLC12A2 | ENSG00000064651 | 0.26 | 0.01 | 0.03 | 0.01 | 0.00 | 0.00 | 0.02 | 0.06 | 0.02 | 0.06 | 0.00 | 0.00 | 0.00 | 0.08 | 0.02 | 0.07 | 0.00 | 0.07 | 0.00 | 0.05 | 0.07 | 0.06 | 0.03 | 0.13 | 0.01 | 0.09 | 0.02 | 0.04 | 0.01 | 0.04 | 0.06 | 0.04 | 0.05 | 0.01 | 0.17 | 0.02 | 0.00 | 0.03 | 0.01 | 0.00 | 0.03 | 0.05 | 0.09 | 0.22 | 0.02 | 0.02 | 0.01 | 0.03 | 0.14 | 0.04 | 0.06 | 0.04 | 0.01 | 0.00 | 0.00 | 0.09 | 0.04 | 0.02 | 0.00 | 0.04 | 0.01 | 0.02 | 0.00 | 0.03 | 0.03 | 0.08 |
| RTN3 | ENSG00000133318 | 0.01 | 0.00 | 0.00 | 0.01 | 0.07 | 0.00 | 0.03 | 0.01 | 0.11 | 0.01 | 0.00 | 0.00 | 0.12 | 0.00 | 0.06 | 0.02 | 0.08 | 0.02 | 0.19 | 0.03 | 0.12 | 0.05 | 0.02 | 0.03 | 0.01 | 0.02 | 0.03 | 0.03 | 0.00 | 0.03 | 0.01 | 0.03 | 0.09 | 0.07 | 0.05 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.09 | 0.08 | 0.16 | 0.04 | 0.07 | 0.01 | 0.10 | 0.01 | 0.51 | 0.12 | 0.08 | 0.02 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.02 | 0.02 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.05 | 0.04 |
| SIRT7 | ENSG00000187531 | 0.02 | 0.00 | 0.05 | 0.00 | 0.02 | 0.00 | 0.03 | 0.02 | 0.22 | 0.00 | 0.00 | 0.00 | 0.12 | 0.02 | 0.17 | 0.02 | 0.19 | 0.07 | 0.07 | 0.06 | 0.12 | 0.10 | 0.11 | 0.04 | 0.05 | 0.00 | 0.04 | 0.02 | 0.02 | 0.09 | 0.31 | 0.01 | 0.15 | 0.01 | 0.27 | 0.00 | 0.03 | 0.01 | 0.00 | 0.00 | 0.33 | 0.05 | 0.41 | 0.06 | 0.10 | 0.09 | 0.18 | 0.01 | 0.74 | 0.08 | 0.18 | 0.11 | 0.06 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.07 | 0.01 | 0.04 | 0.02 | 0.14 | 0.00 | 0.24 | 0.03 |
| SCUBE3 | ENSG00000146197 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.01 | 0.08 | 0.04 | 0.00 | 0.00 | 0.03 | 0.01 | 0.08 | 0.02 | 0.03 | 0.05 | 0.02 | 0.03 | 0.16 | 0.04 | 0.07 | 0.03 | 0.03 | 0.01 | 0.05 | 0.01 | 0.01 | 0.01 | 0.06 | 0.02 | 0.05 | 0.03 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.08 | 0.03 | 0.25 | 0.05 | 0.08 | 0.01 | 0.05 | 0.01 | 0.16 | 0.05 | 0.12 | 0.08 | 0.04 | 0.01 | 0.00 | 0.00 | 0.08 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.10 | 0.00 | 0.10 | 0.00 |
| CAPN9 | ENSG00000135773 | 0.01 | 0.02 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.09 | 0.12 | 0.04 | 0.02 | 0.02 | 0.05 | 0.03 | 0.09 | 0.01 | 0.12 | 0.02 | 0.05 | 0.00 | 0.22 | 0.04 | 0.10 | 0.01 | 0.03 | 0.03 | 0.04 | 0.02 | 0.01 | 0.01 | 0.15 | 0.01 | 0.23 | 0.02 | 0.04 | 0.00 | 0.01 | 0.04 | 0.00 | 0.00 | 0.25 | 0.02 | 0.43 | 0.07 | 0.08 | 0.01 | 0.09 | 0.01 | 0.28 | 0.00 | 0.02 | 0.23 | 0.04 | 0.04 | 0.02 | 0.00 | 0.02 | 0.15 | 0.00 | 0.02 | 0.04 | 0.04 | 0.09 | 0.03 | 0.15 | 0.04 |
| HSD11B1 | ENSG00000117594 | 0.01 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.04 | 0.07 | 0.06 | 0.01 | 0.00 | 0.07 | 0.01 | 0.10 | 0.01 | 0.11 | 0.01 | 0.06 | 0.01 | 0.16 | 0.05 | 0.04 | 0.02 | 0.03 | 0.01 | 0.06 | 0.03 | 0.01 | 0.00 | 0.16 | 0.02 | 0.16 | 0.02 | 0.01 | 0.03 | 0.02 | 0.00 | 0.00 | 0.00 | 0.23 | 0.01 | 0.15 | 0.15 | 0.06 | 0.00 | 0.06 | 0.02 | 0.13 | 0.04 | 0.04 | 0.20 | 0.02 | 0.03 | 0.01 | 0.00 | 0.16 | 0.04 | 0.00 | 0.01 | 0.03 | 0.03 | 0.09 | 0.00 | 0.13 | 0.02 |
| FCER1A | ENSG00000179639 | 0.03 | 0.00 | 0.01 | 0.01 | 0.00 | 0.03 | 0.02 | 0.05 | 0.54 | 0.01 | 0.02 | 0.00 | 0.11 | 0.00 | 0.26 | 0.00 | 0.25 | 0.00 | 0.05 | 0.00 | 0.25 | 0.00 | 0.12 | 0.00 | 0.03 | 0.00 | 0.11 | 0.00 | 0.06 | 0.00 | 0.28 | 0.00 | 0.30 | 0.01 | 0.16 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.25 | 0.01 | 0.38 | 0.02 | 0.16 | 0.00 | 0.13 | 0.00 | 0.28 | 0.00 | 0.38 | 0.02 | 0.10 | 0.00 | 0.00 | 0.00 | 0.24 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.16 | 0.01 |
| DPP4 | ENSG00000197635 | 0.01 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.02 | 0.09 | 0.08 | 0.03 | 0.00 | 0.01 | 0.00 | 0.00 | 0.06 | 0.01 | 0.10 | 0.03 | 0.05 | 0.02 | 0.10 | 0.03 | 0.03 | 0.04 | 0.01 | 0.02 | 0.01 | 0.02 | 0.05 | 0.01 | 0.04 | 0.06 | 0.00 | 0.05 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.03 | 0.29 | 0.04 | 0.05 | 0.01 | 0.05 | 0.01 | 0.03 | 0.00 | 0.05 | 0.08 | 0.03 | 0.01 | 0.00 | 0.00 | 0.00 | 0.15 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.04 | 0.01 |
| CRB1 | ENSG00000134376 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.02 | 0.14 | 0.05 | 0.02 | 0.00 | 0.10 | 0.02 | 0.10 | 0.01 | 0.09 | 0.01 | 0.05 | 0.01 | 0.11 | 0.07 | 0.04 | 0.01 | 0.04 | 0.00 | 0.11 | 0.02 | 0.01 | 0.00 | 0.21 | 0.01 | 0.20 | 0.02 | 0.04 | 0.03 | 0.01 | 0.00 | 0.00 | 0.00 | 0.20 | 0.01 | 0.29 | 0.06 | 0.08 | 0.00 | 0.08 | 0.02 | 0.07 | 0.03 | 0.14 | 0.10 | 0.05 | 0.00 | 0.01 | 0.01 | 0.26 | 0.02 | 0.00 | 0.01 | 0.01 | 0.01 | 0.06 | 0.00 | 0.17 | 0.02 |
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