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 |
| IGFBP7 | ENSG00000163453 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.02 | 0.03 | 0.11 | 0.02 | 0.00 | 0.00 | 0.02 | 0.03 | 0.10 | 0.02 | 0.32 | 0.02 | 0.07 | 0.01 | 0.18 | 0.03 | 0.03 | 0.04 | 0.03 | 0.01 | 0.03 | 0.06 | 0.04 | 0.02 | 0.06 | 0.03 | 0.00 | 0.03 | 0.03 | 0.00 | 0.02 | 0.02 | 0.00 | 0.00 | 0.08 | 0.01 | 0.23 | 0.06 | 0.04 | 0.01 | 0.05 | 0.00 | 0.10 | 0.02 | 0.16 | 0.04 | 0.29 | 0.00 | 0.00 | 0.01 | 0.00 | 0.01 | 0.08 | 0.01 | 0.20 | 0.02 | 0.03 | 0.00 | 0.09 | 0.02 |
| CXCR1 | ENSG00000163464 | 0.02 | 0.07 | 0.04 | 0.04 | 0.00 | 0.03 | 0.02 | 0.01 | 0.01 | 0.26 | 0.00 | 0.00 | 0.00 | 0.12 | 0.03 | 0.03 | 0.05 | 0.19 | 0.01 | 0.18 | 0.04 | 0.11 | 0.07 | 0.03 | 0.02 | 0.01 | 0.02 | 0.02 | 0.05 | 0.03 | 0.04 | 0.05 | 0.00 | 0.01 | 0.07 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.04 | 0.06 | 0.19 | 0.16 | 0.03 | 0.34 | 0.07 | 0.04 | 0.12 | 0.05 | 0.08 | 0.21 | 0.08 | 0.01 | 0.00 | 0.00 | 0.00 | 0.04 | 0.01 | 0.02 | 0.00 | 0.00 | 0.02 | 0.02 | 0.02 | 0.03 |
| ADORA1 | ENSG00000163485 | 0.01 | 0.00 | 0.00 | 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 | 0.15 | 0.06 | 0.06 | 0.01 | 0.04 | 0.00 | 0.11 | 0.02 | 0.00 | 0.00 | 0.20 | 0.01 | 0.18 | 0.02 | 0.04 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.26 | 0.00 | 0.32 | 0.07 | 0.06 | 0.00 | 0.10 | 0.01 | 0.17 | 0.00 | 0.10 | 0.12 | 0.05 | 0.00 | 0.01 | 0.00 | 0.26 | 0.02 | 0.04 | 0.01 | 0.12 | 0.00 | 0.09 | 0.00 | 0.18 | 0.01 |
| NEK10 | ENSG00000163491 | 0.01 | 0.18 | 0.00 | 0.01 | 0.09 | 0.00 | 0.00 | 0.02 | 0.17 | 0.04 | 0.00 | 0.03 | 0.02 | 0.11 | 0.01 | 0.04 | 0.01 | 0.04 | 0.00 | 0.05 | 0.04 | 0.04 | 0.04 | 0.06 | 0.00 | 0.03 | 0.03 | 0.02 | 0.02 | 0.03 | 0.06 | 0.01 | 0.00 | 0.16 | 0.05 | 0.01 | 0.01 | 0.03 | 0.00 | 0.00 | 0.07 | 0.05 | 0.12 | 0.18 | 0.03 | 0.02 | 0.04 | 0.03 | 0.12 | 0.11 | 0.11 | 0.02 | 0.05 | 0.04 | 0.00 | 0.01 | 0.04 | 0.01 | 0.02 | 0.01 | 0.00 | 0.02 | 0.00 | 0.03 | 0.05 | 0.04 |
| IHH | ENSG00000163501 | 0.01 | 0.06 | 0.04 | 0.04 | 0.00 | 0.03 | 0.01 | 0.02 | 0.01 | 0.27 | 0.00 | 0.01 | 0.00 | 0.10 | 0.02 | 0.03 | 0.04 | 0.19 | 0.00 | 0.18 | 0.03 | 0.13 | 0.06 | 0.04 | 0.02 | 0.01 | 0.02 | 0.02 | 0.05 | 0.03 | 0.03 | 0.04 | 0.00 | 0.01 | 0.04 | 0.02 | 0.00 | 0.00 | 0.00 | 0.01 | 0.04 | 0.06 | 0.18 | 0.16 | 0.03 | 0.34 | 0.06 | 0.05 | 0.12 | 0.05 | 0.08 | 0.19 | 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 | 0.03 |
| RETNLB | ENSG00000163515 | 0.00 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.04 | 0.03 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.05 | 0.01 | 0.17 | 0.03 | 0.05 | 0.01 | 0.07 | 0.03 | 0.06 | 0.02 | 0.00 | 0.01 | 0.01 | 0.02 | 0.00 | 0.01 | 0.01 | 0.01 | 0.00 | 0.01 | 0.10 | 0.02 | 0.00 | 0.06 | 0.00 | 0.00 | 0.05 | 0.02 | 0.31 | 0.03 | 0.04 | 0.01 | 0.03 | 0.01 | 0.14 | 0.08 | 0.12 | 0.06 | 0.03 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.03 | 0.01 | 0.05 | 0.00 | 0.00 | 0.02 | 0.03 |
| FCRL4 | ENSG00000163518 | 0.03 | 0.00 | 0.01 | 0.01 | 0.00 | 0.03 | 0.02 | 0.06 | 0.36 | 0.02 | 0.02 | 0.00 | 0.11 | 0.00 | 0.28 | 0.00 | 0.24 | 0.00 | 0.07 | 0.00 | 0.25 | 0.00 | 0.12 | 0.00 | 0.03 | 0.00 | 0.11 | 0.00 | 0.07 | 0.00 | 0.31 | 0.00 | 0.41 | 0.01 | 0.05 | 0.02 | 0.04 | 0.00 | 0.00 | 0.00 | 0.26 | 0.01 | 0.39 | 0.02 | 0.15 | 0.00 | 0.14 | 0.00 | 0.37 | 0.00 | 0.44 | 0.01 | 0.10 | 0.00 | 0.00 | 0.00 | 0.25 | 0.00 | 0.01 | 0.00 | 0.05 | 0.00 | 0.00 | 0.03 | 0.17 | 0.01 |
| FCRL1 | ENSG00000163534 | 0.03 | 0.00 | 0.01 | 0.01 | 0.00 | 0.03 | 0.02 | 0.07 | 0.40 | 0.01 | 0.02 | 0.00 | 0.11 | 0.00 | 0.26 | 0.00 | 0.24 | 0.01 | 0.07 | 0.00 | 0.25 | 0.00 | 0.12 | 0.00 | 0.03 | 0.00 | 0.11 | 0.00 | 0.07 | 0.00 | 0.30 | 0.00 | 0.41 | 0.01 | 0.05 | 0.02 | 0.04 | 0.00 | 0.00 | 0.00 | 0.27 | 0.01 | 0.38 | 0.02 | 0.15 | 0.00 | 0.15 | 0.00 | 0.37 | 0.00 | 0.37 | 0.01 | 0.10 | 0.00 | 0.00 | 0.00 | 0.25 | 0.00 | 0.01 | 0.00 | 0.05 | 0.00 | 0.00 | 0.03 | 0.18 | 0.02 |
| SLC2A2 | ENSG00000163581 | 0.05 | 0.01 | 0.03 | 0.00 | 0.00 | 0.00 | 0.08 | 0.01 | 0.18 | 0.01 | 0.00 | 0.00 | 0.00 | 0.03 | 0.23 | 0.01 | 1.74 | 0.00 | 0.61 | 0.00 | 0.88 | 0.01 | 0.29 | 0.00 | 0.03 | 0.01 | 0.04 | 0.01 | 0.05 | 0.00 | 0.15 | 0.02 | 0.12 | 0.03 | 0.10 | 0.00 | 0.00 | 0.09 | 0.00 | 0.00 | 0.24 | 0.01 | 1.37 | 0.02 | 0.76 | 0.00 | 0.37 | 0.00 | 1.05 | 0.06 | 0.06 | 0.08 | 0.19 | 0.00 | 0.00 | 0.00 | 0.06 | 0.00 | 0.03 | 0.01 | 0.05 | 0.02 | 0.00 | 0.00 | 0.03 | 0.02 |
| FABP1 | ENSG00000163586 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.03 | 0.08 | 0.01 | 0.00 | 0.00 | 0.02 | 0.03 | 0.03 | 0.02 | 0.08 | 0.02 | 0.06 | 0.01 | 0.09 | 0.01 | 0.01 | 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 | 0.10 | 0.04 | 0.04 | 0.01 | 0.04 | 0.02 | 0.08 | 0.02 | 0.18 | 0.04 | 0.01 | 0.04 | 0.00 | 0.00 | 0.00 | 0.04 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.02 | 0.01 |
| ICOS | ENSG00000163600 | 0.02 | 0.03 | 0.04 | 0.02 | 0.00 | 0.03 | 0.01 | 0.02 | 0.02 | 0.13 | 0.00 | 0.00 | 0.00 | 0.06 | 0.05 | 0.02 | 0.13 | 0.09 | 0.08 | 0.12 | 0.13 | 0.05 | 0.08 | 0.02 | 0.02 | 0.01 | 0.03 | 0.00 | 0.07 | 0.01 | 0.09 | 0.01 | 0.00 | 0.01 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.03 | 0.24 | 0.10 | 0.05 | 0.24 | 0.05 | 0.02 | 0.06 | 0.05 | 0.08 | 0.09 | 0.06 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.00 | 0.01 | 0.01 | 0.00 | 0.02 | 0.02 | 0.02 | 0.02 |
| RYBP | ENSG00000163602 | 0.00 | 0.02 | 0.00 | 0.01 | 0.00 | 0.02 | 0.01 | 0.21 | 0.04 | 0.16 | 0.01 | 0.04 | 0.01 | 0.11 | 0.05 | 0.06 | 0.00 | 0.18 | 0.02 | 0.09 | 0.04 | 0.15 | 0.08 | 0.05 | 0.01 | 0.01 | 0.03 | 0.03 | 0.01 | 0.02 | 0.01 | 0.08 | 0.00 | 0.21 | 0.08 | 0.01 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.14 | 0.13 | 0.12 | 0.00 | 0.13 | 0.04 | 0.07 | 0.26 | 0.26 | 0.04 | 0.11 | 0.10 | 0.00 | 0.00 | 0.03 | 0.02 | 0.00 | 0.00 | 0.03 | 0.00 | 0.02 | 0.00 | 0.03 | 0.19 | 0.01 |
| PTX3 | ENSG00000163661 | 0.04 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.05 | 0.01 | 0.11 | 0.01 | 0.00 | 0.00 | 0.00 | 0.04 | 0.13 | 0.02 | 0.94 | 0.01 | 0.47 | 0.00 | 0.66 | 0.02 | 0.16 | 0.01 | 0.02 | 0.00 | 0.05 | 0.01 | 0.03 | 0.00 | 0.08 | 0.01 | 0.03 | 0.01 | 0.10 | 0.01 | 0.00 | 0.06 | 0.00 | 0.00 | 0.15 | 0.01 | 0.72 | 0.02 | 0.49 | 0.01 | 0.16 | 0.01 | 0.21 | 0.02 | 0.06 | 0.07 | 0.11 | 0.00 | 0.00 | 0.00 | 0.04 | 0.00 | 0.02 | 0.01 | 0.03 | 0.04 | 0.00 | 0.00 | 0.01 | 0.03 |
| DCLK3 | ENSG00000163673 | 0.00 | 0.18 | 0.00 | 0.01 | 0.08 | 0.00 | 0.00 | 0.01 | 0.12 | 0.04 | 0.00 | 0.02 | 0.02 | 0.25 | 0.01 | 0.04 | 0.03 | 0.04 | 0.00 | 0.04 | 0.03 | 0.04 | 0.04 | 0.08 | 0.00 | 0.02 | 0.03 | 0.02 | 0.01 | 0.02 | 0.04 | 0.02 | 0.00 | 0.20 | 0.06 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.04 | 0.08 | 0.12 | 0.16 | 0.02 | 0.02 | 0.02 | 0.03 | 0.13 | 0.13 | 0.10 | 0.05 | 0.04 | 0.04 | 0.00 | 0.01 | 0.04 | 0.09 | 0.01 | 0.02 | 0.00 | 0.03 | 0.00 | 0.03 | 0.03 | 0.05 |
| DNASE1L3 | ENSG00000163687 | 0.00 | 0.11 | 0.00 | 0.02 | 0.00 | 0.02 | 0.01 | 0.02 | 0.03 | 0.14 | 0.01 | 0.02 | 0.00 | 0.35 | 0.00 | 0.05 | 0.01 | 0.11 | 0.00 | 0.06 | 0.02 | 0.14 | 0.02 | 0.08 | 0.01 | 0.04 | 0.02 | 0.06 | 0.00 | 0.03 | 0.03 | 0.06 | 0.00 | 0.17 | 0.07 | 0.01 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.17 | 0.13 | 0.17 | 0.00 | 0.10 | 0.01 | 0.07 | 0.19 | 0.32 | 0.04 | 0.14 | 0.06 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.03 | 0.00 | 0.00 | 0.07 | 0.02 |
| PCOLCE2 | ENSG00000163710 | 0.04 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.07 | 0.02 | 0.08 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.07 | 0.01 | 0.54 | 0.01 | 0.30 | 0.00 | 0.36 | 0.01 | 0.11 | 0.01 | 0.01 | 0.01 | 0.04 | 0.00 | 0.00 | 0.00 | 0.06 | 0.01 | 0.00 | 0.03 | 0.09 | 0.01 | 0.00 | 0.05 | 0.00 | 0.00 | 0.10 | 0.02 | 0.53 | 0.02 | 0.31 | 0.01 | 0.11 | 0.00 | 0.27 | 0.02 | 0.07 | 0.09 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.02 | 0.00 | 0.01 | 0.03 | 0.03 | 0.00 | 0.00 | 0.01 | 0.04 |
| CXCL3 | ENSG00000163734 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.04 | 0.01 | 0.13 | 0.02 | 0.00 | 0.00 | 0.00 | 0.06 | 0.07 | 0.02 | 0.22 | 0.01 | 0.10 | 0.01 | 0.23 | 0.02 | 0.09 | 0.02 | 0.02 | 0.01 | 0.05 | 0.01 | 0.01 | 0.00 | 0.02 | 0.08 | 0.00 | 0.03 | 0.11 | 0.00 | 0.04 | 0.02 | 0.00 | 0.00 | 0.16 | 0.02 | 0.30 | 0.12 | 0.06 | 0.03 | 0.04 | 0.01 | 0.05 | 0.05 | 0.07 | 0.06 | 0.09 | 0.03 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.03 |
| CXCL5 | ENSG00000163735 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.04 | 0.01 | 0.14 | 0.02 | 0.00 | 0.00 | 0.00 | 0.06 | 0.07 | 0.02 | 0.22 | 0.01 | 0.09 | 0.01 | 0.23 | 0.02 | 0.08 | 0.02 | 0.02 | 0.01 | 0.05 | 0.01 | 0.01 | 0.00 | 0.02 | 0.08 | 0.00 | 0.03 | 0.11 | 0.00 | 0.02 | 0.02 | 0.00 | 0.00 | 0.16 | 0.02 | 0.30 | 0.11 | 0.06 | 0.03 | 0.04 | 0.01 | 0.05 | 0.05 | 0.07 | 0.06 | 0.09 | 0.01 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.03 |
| PPBP | ENSG00000163736 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.04 | 0.01 | 0.14 | 0.02 | 0.00 | 0.00 | 0.00 | 0.06 | 0.07 | 0.02 | 0.22 | 0.01 | 0.09 | 0.01 | 0.23 | 0.02 | 0.08 | 0.02 | 0.02 | 0.01 | 0.05 | 0.01 | 0.01 | 0.00 | 0.02 | 0.08 | 0.00 | 0.03 | 0.11 | 0.00 | 0.02 | 0.02 | 0.00 | 0.00 | 0.16 | 0.02 | 0.30 | 0.11 | 0.06 | 0.03 | 0.04 | 0.01 | 0.05 | 0.05 | 0.07 | 0.06 | 0.09 | 0.01 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.03 |
| PF4 | ENSG00000163737 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.04 | 0.01 | 0.16 | 0.01 | 0.00 | 0.00 | 0.00 | 0.06 | 0.07 | 0.02 | 0.22 | 0.01 | 0.09 | 0.01 | 0.23 | 0.02 | 0.08 | 0.02 | 0.02 | 0.01 | 0.05 | 0.01 | 0.01 | 0.00 | 0.02 | 0.08 | 0.00 | 0.03 | 0.11 | 0.00 | 0.02 | 0.02 | 0.00 | 0.00 | 0.16 | 0.02 | 0.30 | 0.11 | 0.06 | 0.03 | 0.04 | 0.01 | 0.05 | 0.05 | 0.07 | 0.06 | 0.09 | 0.01 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.03 |
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