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 |
| ITLN1 | ENSG00000179914 | 0.03 | 0.00 | 0.02 | 0.01 | 0.00 | 0.03 | 0.02 | 0.05 | 0.91 | 0.00 | 0.02 | 0.00 | 0.10 | 0.02 | 0.27 | 0.00 | 0.28 | 0.00 | 0.06 | 0.00 | 0.28 | 0.00 | 0.14 | 0.00 | 0.03 | 0.00 | 0.12 | 0.00 | 0.06 | 0.00 | 0.30 | 0.00 | 0.30 | 0.01 | 0.16 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.32 | 0.00 | 0.37 | 0.02 | 0.18 | 0.00 | 0.14 | 0.00 | 0.41 | 0.00 | 0.46 | 0.02 | 0.11 | 0.00 | 0.00 | 0.00 | 0.25 | 0.00 | 0.01 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.16 | 0.01 |
| SLC27A5 | ENSG00000083807 | 0.01 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.00 | 0.15 | 0.04 | 0.00 | 0.00 | 0.03 | 0.04 | 0.04 | 0.07 | 0.13 | 0.09 | 0.07 | 0.05 | 0.25 | 0.06 | 0.15 | 0.03 | 0.02 | 0.03 | 0.02 | 0.04 | 0.05 | 0.04 | 0.07 | 0.03 | 0.02 | 0.07 | 0.14 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.15 | 0.06 | 0.18 | 0.35 | 0.12 | 0.05 | 0.08 | 0.07 | 0.14 | 0.12 | 0.07 | 0.30 | 0.00 | 0.06 | 0.02 | 0.01 | 0.16 | 0.03 | 0.01 | 0.17 | 0.05 | 0.12 | 0.00 | 0.00 | 0.04 | 0.06 |
| FASN | ENSG00000169710 | 0.02 | 0.00 | 0.05 | 0.00 | 0.02 | 0.00 | 0.03 | 0.02 | 0.21 | 0.01 | 0.00 | 0.00 | 0.12 | 0.02 | 0.17 | 0.02 | 0.19 | 0.08 | 0.06 | 0.07 | 0.12 | 0.11 | 0.11 | 0.04 | 0.05 | 0.00 | 0.04 | 0.03 | 0.03 | 0.09 | 0.31 | 0.03 | 0.15 | 0.01 | 0.30 | 0.00 | 0.03 | 0.01 | 0.00 | 0.00 | 0.34 | 0.05 | 0.42 | 0.07 | 0.09 | 0.09 | 0.16 | 0.02 | 0.63 | 0.08 | 0.21 | 0.14 | 0.06 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.07 | 0.01 | 0.03 | 0.02 | 0.20 | 0.00 | 0.24 | 0.03 |
| SERPINB5 | ENSG00000206075 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.11 | 0.01 | 0.09 | 0.00 | 0.00 | 0.00 | 0.02 | 0.03 | 0.09 | 0.05 | 0.06 | 0.02 | 0.14 | 0.05 | 0.20 | 0.02 | 0.16 | 0.00 | 0.12 | 0.01 | 0.09 | 0.00 | 0.08 | 0.02 | 0.06 | 0.00 | 0.10 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.09 | 0.05 | 0.09 | 0.32 | 0.03 | 0.03 | 0.01 | 0.07 | 0.01 | 0.11 | 0.12 | 0.08 | 0.00 | 0.07 | 0.00 | 0.01 | 0.10 | 0.00 | 0.01 | 0.02 | 0.00 | 0.03 | 0.00 | 0.01 | 0.03 | 0.02 |
| HM13 | ENSG00000101294 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.02 | 0.00 | 0.33 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 | 0.13 | 0.01 | 0.28 | 0.00 | 0.20 | 0.00 | 0.10 | 0.00 | 0.08 | 0.00 | 0.18 | 0.00 | 0.23 | 0.00 | 0.01 | 0.01 | 0.03 | 0.00 | 0.00 | 0.01 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.08 | 0.01 | 0.34 | 0.02 | 0.28 | 0.00 | 0.18 | 0.00 | 1.28 | 0.00 | 0.14 | 0.02 | 0.23 | 0.00 | 0.05 | 0.00 | 0.08 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.04 | 0.01 |
| FDFT1 | ENSG00000079459 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.01 | 0.01 | 0.16 | 0.02 | 0.14 | 0.00 | 0.00 | 0.02 | 0.01 | 0.04 | 0.07 | 0.01 | 0.10 | 0.00 | 0.08 | 0.54 | 0.04 | 0.43 | 0.02 | 0.01 | 0.10 | 0.00 | 0.15 | 0.06 | 0.05 | 0.01 | 0.11 | 0.00 | 0.01 | 0.06 | 0.02 | 0.00 | 0.03 | 0.00 | 0.00 | 0.01 | 0.16 | 0.04 | 0.42 | 0.01 | 0.04 | 0.00 | 0.09 | 0.07 | 0.24 | 0.06 | 0.09 | 0.03 | 0.01 | 0.00 | 0.00 | 0.04 | 0.09 | 0.00 | 0.02 | 0.01 | 0.03 | 0.00 | 0.01 | 0.02 | 0.03 |
| NR5A2 | ENSG00000116833 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.12 | 0.05 | 0.02 | 0.00 | 0.10 | 0.00 | 0.13 | 0.00 | 0.08 | 0.02 | 0.05 | 0.01 | 0.12 | 0.06 | 0.05 | 0.01 | 0.04 | 0.01 | 0.06 | 0.05 | 0.01 | 0.00 | 0.24 | 0.01 | 0.20 | 0.02 | 0.04 | 0.04 | 0.01 | 0.00 | 0.00 | 0.00 | 0.22 | 0.01 | 0.28 | 0.06 | 0.07 | 0.00 | 0.07 | 0.02 | 0.07 | 0.03 | 0.10 | 0.12 | 0.07 | 0.00 | 0.01 | 0.01 | 0.26 | 0.02 | 0.00 | 0.01 | 0.02 | 0.01 | 0.06 | 0.00 | 0.19 | 0.01 |
| IKBKB | ENSG00000104365 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.10 | 0.21 | 0.05 | 0.00 | 0.00 | 0.04 | 0.00 | 0.21 | 0.04 | 0.40 | 0.03 | 0.11 | 0.03 | 0.45 | 0.07 | 0.08 | 0.04 | 0.18 | 0.02 | 0.19 | 0.04 | 0.02 | 0.00 | 0.04 | 0.04 | 0.00 | 0.02 | 0.09 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.41 | 0.05 | 0.37 | 0.04 | 0.08 | 0.03 | 0.20 | 0.01 | 0.80 | 0.07 | 0.14 | 0.07 | 0.02 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.00 | 0.01 | 0.05 | 0.02 |
| SEZ6L2 | ENSG00000174938 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.17 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.09 | 0.01 | 0.09 | 0.01 | 0.03 | 0.01 | 0.12 | 0.00 | 0.05 | 0.00 | 0.05 | 0.00 | 0.05 | 0.00 | 0.00 | 0.00 | 0.04 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.08 | 0.01 | 0.12 | 0.03 | 0.02 | 0.02 | 0.10 | 0.01 | 0.34 | 0.05 | 0.04 | 0.04 | 0.00 | 0.02 | 0.00 | 0.01 | 0.02 | 0.00 | 0.00 | 0.01 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.02 |
| GRIN2D | ENSG00000105464 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.04 | 0.07 | 0.04 | 0.00 | 0.02 | 0.00 | 0.08 | 0.01 | 0.08 | 0.04 | 0.10 | 0.02 | 0.02 | 0.09 | 0.05 | 0.06 | 0.03 | 0.01 | 0.02 | 0.01 | 0.04 | 0.04 | 0.05 | 0.04 | 0.04 | 0.00 | 0.07 | 0.18 | 0.02 | 0.00 | 0.03 | 0.00 | 0.00 | 0.06 | 0.05 | 0.07 | 0.32 | 0.05 | 0.07 | 0.05 | 0.06 | 0.14 | 0.22 | 0.04 | 0.17 | 0.00 | 0.04 | 0.01 | 0.00 | 0.07 | 0.03 | 0.00 | 0.13 | 0.01 | 0.13 | 0.00 | 0.00 | 0.03 | 0.02 |
| ATP6V1D | ENSG00000100554 | 0.01 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.04 | 0.05 | 0.06 | 0.00 | 0.01 | 0.02 | 0.06 | 0.02 | 0.04 | 0.02 | 0.06 | 0.08 | 0.01 | 0.13 | 0.04 | 0.04 | 0.08 | 0.00 | 0.04 | 0.02 | 0.03 | 0.01 | 0.00 | 0.01 | 0.11 | 0.00 | 0.33 | 0.01 | 0.03 | 0.02 | 0.03 | 0.00 | 0.00 | 0.03 | 0.10 | 0.06 | 0.26 | 0.02 | 0.03 | 0.01 | 0.03 | 0.10 | 0.06 | 0.04 | 0.13 | 0.02 | 0.01 | 0.00 | 0.00 | 0.04 | 0.00 | 0.00 | 0.11 | 0.01 | 0.08 | 0.03 | 0.00 | 0.02 | 0.05 |
| PRKCA | ENSG00000154229 | 0.02 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 | 0.23 | 0.02 | 0.02 | 0.00 | 0.12 | 0.00 | 0.14 | 0.01 | 0.19 | 0.01 | 0.07 | 0.02 | 0.25 | 0.06 | 0.11 | 0.03 | 0.10 | 0.01 | 0.10 | 0.01 | 0.05 | 0.11 | 0.21 | 0.01 | 0.12 | 0.01 | 0.15 | 0.10 | 0.02 | 0.01 | 0.00 | 0.00 | 0.54 | 0.02 | 0.25 | 0.04 | 0.17 | 0.03 | 0.11 | 0.02 | 0.45 | 0.02 | 0.24 | 0.04 | 0.02 | 0.00 | 0.00 | 0.01 | 0.05 | 0.07 | 0.07 | 0.00 | 0.03 | 0.00 | 0.17 | 0.01 | 0.24 | 0.01 |
| SLC3A1 | ENSG00000138079 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.07 | 0.06 | 0.00 | 0.00 | 0.00 | 0.01 | 0.05 | 0.07 | 0.01 | 0.16 | 0.02 | 0.03 | 0.01 | 0.05 | 0.02 | 0.03 | 0.03 | 0.00 | 0.02 | 0.01 | 0.02 | 0.01 | 0.02 | 0.06 | 0.02 | 0.00 | 0.05 | 0.02 | 0.07 | 0.00 | 0.01 | 0.00 | 0.00 | 0.05 | 0.02 | 0.27 | 0.05 | 0.07 | 0.00 | 0.08 | 0.02 | 0.20 | 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 | 0.01 | 0.01 |
| HMGCS1 | ENSG00000112972 | 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 | 0.19 | 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 | 0.09 | 0.01 | 0.25 | 0.03 | 0.20 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 | 0.00 | 0.00 | 0.01 | 0.00 | 0.02 | 0.00 | 0.00 | 0.10 | 0.02 |
| RB1 | ENSG00000139687 | 0.00 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.39 | 0.02 | 0.34 | 0.00 | 0.00 | 0.00 | 0.19 | 0.01 | 0.08 | 0.02 | 0.18 | 0.02 | 0.15 | 0.05 | 0.16 | 0.12 | 0.05 | 0.10 | 0.04 | 0.10 | 0.04 | 0.01 | 0.03 | 0.00 | 0.35 | 0.00 | 0.09 | 0.00 | 0.21 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.20 | 0.04 | 0.44 | 0.01 | 0.24 | 0.02 | 0.08 | 0.03 | 0.44 | 0.01 | 0.76 | 0.00 | 0.02 | 0.00 | 0.00 | 0.03 | 0.23 | 0.01 | 0.09 | 0.00 | 0.19 | 0.00 | 0.00 | 0.02 | 0.05 |
| SLC6A17 | ENSG00000197106 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.06 | 0.05 | 0.06 | 0.00 | 0.00 | 0.00 | 0.33 | 0.01 | 0.13 | 0.02 | 0.14 | 0.00 | 0.12 | 0.06 | 0.12 | 0.02 | 0.07 | 0.00 | 0.06 | 0.00 | 0.07 | 0.00 | 0.02 | 0.02 | 0.03 | 0.00 | 0.11 | 0.06 | 0.04 | 0.00 | 0.26 | 0.00 | 0.00 | 0.04 | 0.10 | 0.16 | 0.15 | 0.01 | 0.07 | 0.03 | 0.03 | 0.06 | 0.06 | 0.05 | 0.10 | 0.03 | 0.04 | 0.00 | 0.00 | 0.00 | 0.05 | 0.00 | 0.01 | 0.01 | 0.02 | 0.00 | 0.03 | 0.08 | 0.10 |
| ROS1 | ENSG00000047936 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.25 | 0.02 | 0.11 | 0.00 | 0.01 | 0.02 | 0.15 | 0.02 | 0.06 | 0.03 | 0.04 | 0.03 | 0.03 | 0.09 | 0.07 | 0.03 | 0.05 | 0.01 | 0.04 | 0.01 | 0.03 | 0.00 | 0.04 | 0.03 | 0.07 | 0.00 | 0.16 | 0.06 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.09 | 0.07 | 0.07 | 0.26 | 0.01 | 0.02 | 0.06 | 0.02 | 0.07 | 0.05 | 0.21 | 0.06 | 0.00 | 0.03 | 0.00 | 0.00 | 0.01 | 0.18 | 0.00 | 0.04 | 0.01 | 0.10 | 0.04 | 0.03 | 0.01 | 0.13 |
| ADAM12 | ENSG00000148848 | 0.00 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.06 | 0.05 | 0.10 | 0.00 | 0.02 | 0.02 | 0.16 | 0.04 | 0.04 | 0.06 | 0.07 | 0.02 | 0.03 | 0.08 | 0.06 | 0.12 | 0.06 | 0.01 | 0.07 | 0.02 | 0.05 | 0.01 | 0.02 | 0.02 | 0.10 | 0.14 | 0.11 | 0.11 | 0.01 | 0.02 | 0.02 | 0.00 | 0.00 | 0.08 | 0.09 | 0.25 | 0.19 | 0.02 | 0.05 | 0.05 | 0.06 | 0.11 | 0.10 | 0.09 | 0.06 | 0.08 | 0.04 | 0.00 | 0.00 | 0.03 | 0.05 | 0.01 | 0.14 | 0.02 | 0.07 | 0.00 | 0.00 | 0.01 | 0.05 |
| STYK1 | ENSG00000060140 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.14 | 0.06 | 0.06 | 0.01 | 0.00 | 0.00 | 0.05 | 0.04 | 0.09 | 0.13 | 0.01 | 0.10 | 0.02 | 0.06 | 0.02 | 0.05 | 0.08 | 0.01 | 0.03 | 0.04 | 0.04 | 0.01 | 0.07 | 0.01 | 0.05 | 0.14 | 0.05 | 0.03 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.10 | 0.05 | 0.31 | 0.10 | 0.02 | 0.02 | 0.03 | 0.03 | 0.04 | 0.03 | 0.08 | 0.13 | 0.56 | 0.00 | 0.00 | 0.03 | 0.00 | 0.04 | 0.10 | 0.01 | 0.02 | 0.05 | 0.00 | 0.01 | 0.05 | 0.03 |
| RAF1 | ENSG00000132155 | 0.00 | 0.18 | 0.00 | 0.01 | 0.07 | 0.00 | 0.01 | 0.02 | 0.64 | 0.01 | 0.00 | 0.03 | 0.03 | 0.05 | 0.03 | 0.04 | 0.02 | 0.03 | 0.02 | 0.02 | 0.05 | 0.03 | 0.08 | 0.04 | 0.02 | 0.04 | 0.03 | 0.07 | 0.02 | 0.02 | 0.08 | 0.01 | 0.00 | 0.18 | 0.07 | 0.01 | 0.00 | 0.04 | 0.00 | 0.00 | 0.12 | 0.03 | 0.14 | 0.21 | 0.03 | 0.01 | 0.07 | 0.03 | 0.05 | 0.14 | 0.24 | 0.02 | 0.04 | 0.05 | 0.00 | 0.01 | 0.00 | 0.05 | 0.03 | 0.01 | 0.03 | 0.02 | 0.00 | 0.00 | 0.04 | 0.05 |
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