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 |
| GFER | ENSG00000127554 | 0.01 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.02 | 0.15 | 0.00 | 0.00 | 0.04 | 0.04 | 0.04 | 0.04 | 0.03 | 0.08 | 0.04 | 0.03 | 0.04 | 0.09 | 0.04 | 0.07 | 0.03 | 0.03 | 0.04 | 0.03 | 0.02 | 0.02 | 0.06 | 0.03 | 0.00 | 0.05 | 0.16 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.10 | 0.02 | 0.10 | 0.18 | 0.10 | 0.04 | 0.07 | 0.03 | 0.28 | 0.08 | 0.10 | 0.04 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.02 | 0.02 | 0.00 | 0.00 | 0.04 | 0.02 |
| WFIKKN1 | ENSG00000127578 | 0.01 | 0.00 | 0.02 | 0.01 | 0.00 | 0.00 | 0.02 | 0.02 | 0.03 | 0.15 | 0.00 | 0.00 | 0.04 | 0.02 | 0.06 | 0.05 | 0.05 | 0.09 | 0.03 | 0.03 | 0.02 | 0.14 | 0.05 | 0.09 | 0.03 | 0.04 | 0.03 | 0.03 | 0.01 | 0.03 | 0.03 | 0.06 | 0.00 | 0.05 | 0.14 | 0.02 | 0.00 | 0.02 | 0.00 | 0.00 | 0.08 | 0.03 | 0.14 | 0.22 | 0.10 | 0.06 | 0.09 | 0.05 | 0.14 | 0.21 | 0.08 | 0.09 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.06 | 0.01 | 0.00 | 0.02 | 0.03 | 0.00 | 0.00 | 0.04 | 0.04 |
| OR1E2 | ENSG00000127780 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.06 | 0.04 | 0.03 | 0.00 | 0.00 | 0.01 | 0.02 | 0.01 | 0.06 | 0.02 | 0.02 | 0.01 | 0.03 | 0.04 | 0.04 | 0.01 | 0.02 | 0.01 | 0.01 | 0.00 | 0.01 | 0.00 | 0.03 | 0.01 | 0.12 | 0.00 | 0.08 | 0.02 | 0.03 | 0.00 | 0.03 | 0.00 | 0.00 | 0.03 | 0.05 | 0.13 | 0.09 | 0.01 | 0.03 | 0.03 | 0.04 | 0.06 | 0.13 | 0.15 | 0.23 | 0.00 | 0.02 | 0.00 | 0.03 | 0.00 | 0.06 | 0.00 | 0.00 | 0.00 | 0.05 | 0.00 | 0.00 | 0.02 | 0.03 |
| TUBA4A | ENSG00000127824 | 0.01 | 0.07 | 0.04 | 0.04 | 0.00 | 0.03 | 0.01 | 0.02 | 0.01 | 0.27 | 0.00 | 0.01 | 0.00 | 0.10 | 0.03 | 0.03 | 0.04 | 0.19 | 0.00 | 0.18 | 0.03 | 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 | 0.06 | 0.04 | 0.08 | 0.05 | 0.09 | 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 | 0.04 |
| FGL2 | ENSG00000127951 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 | 0.03 | 0.02 | 0.00 | 0.00 | 0.02 | 0.00 | 0.04 | 0.02 | 0.12 | 0.02 | 0.06 | 0.02 | 0.13 | 0.03 | 0.09 | 0.01 | 0.01 | 0.01 | 0.01 | 0.00 | 0.02 | 0.01 | 0.05 | 0.01 | 0.00 | 0.01 | 0.03 | 0.01 | 0.00 | 0.02 | 0.00 | 0.00 | 0.06 | 0.03 | 0.17 | 0.08 | 0.04 | 0.01 | 0.05 | 0.03 | 0.08 | 0.03 | 0.06 | 0.06 | 0.09 | 0.00 | 0.00 | 0.00 | 0.10 | 0.00 | 0.03 | 0.01 | 0.06 | 0.01 | 0.00 | 0.00 | 0.05 | 0.02 |
| SRD5A3 | ENSG00000128039 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.01 | 0.02 | 0.12 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.10 | 0.02 | 0.49 | 0.01 | 0.09 | 0.00 | 0.15 | 0.05 | 0.04 | 0.03 | 0.03 | 0.01 | 0.02 | 0.03 | 0.02 | 0.02 | 0.03 | 0.04 | 0.00 | 0.08 | 0.03 | 0.00 | 0.02 | 0.02 | 0.00 | 0.00 | 0.09 | 0.01 | 0.21 | 0.04 | 0.13 | 0.01 | 0.04 | 0.00 | 0.15 | 0.05 | 0.22 | 0.03 | 0.37 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.13 | 0.01 | 0.36 | 0.01 | 0.00 | 0.00 | 0.10 | 0.01 |
| SPINK2 | ENSG00000128040 | 0.01 | 0.01 | 0.01 | 0.00 | 0.01 | 0.00 | 0.02 | 0.02 | 0.10 | 0.02 | 0.00 | 0.00 | 0.02 | 0.03 | 0.10 | 0.02 | 0.34 | 0.02 | 0.08 | 0.01 | 0.16 | 0.03 | 0.03 | 0.03 | 0.02 | 0.01 | 0.03 | 0.06 | 0.04 | 0.02 | 0.03 | 0.02 | 0.00 | 0.03 | 0.03 | 0.00 | 0.02 | 0.02 | 0.00 | 0.00 | 0.07 | 0.01 | 0.22 | 0.06 | 0.04 | 0.01 | 0.05 | 0.00 | 0.10 | 0.02 | 0.16 | 0.03 | 0.31 | 0.00 | 0.00 | 0.01 | 0.00 | 0.01 | 0.08 | 0.01 | 0.22 | 0.01 | 0.03 | 0.00 | 0.08 | 0.02 |
| KDR | ENSG00000128052 | 0.01 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.01 | 0.02 | 0.13 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.12 | 0.02 | 0.45 | 0.01 | 0.08 | 0.01 | 0.15 | 0.05 | 0.04 | 0.03 | 0.03 | 0.01 | 0.02 | 0.03 | 0.02 | 0.02 | 0.03 | 0.04 | 0.00 | 0.08 | 0.03 | 0.00 | 0.02 | 0.02 | 0.00 | 0.00 | 0.09 | 0.01 | 0.20 | 0.05 | 0.10 | 0.01 | 0.04 | 0.00 | 0.20 | 0.05 | 0.22 | 0.03 | 0.37 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.13 | 0.00 | 0.42 | 0.01 | 0.00 | 0.00 | 0.11 | 0.01 |
| ADM2 | ENSG00000128165 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.03 | 0.01 | 0.03 | 0.01 | 0.12 | 0.00 | 0.03 | 0.00 | 0.06 | 0.02 | 0.12 | 0.06 | 0.09 | 0.02 | 0.04 | 0.03 | 0.03 | 0.03 | 0.07 | 0.00 | 0.04 | 0.01 | 0.09 | 0.01 | 0.10 | 0.07 | 0.07 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.06 | 0.00 | 0.01 | 0.06 | 0.06 | 0.02 | 0.64 | 0.03 | 0.07 | 0.03 | 0.15 | 0.06 | 0.27 | 0.06 | 0.15 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.09 | 0.00 | 0.05 | 0.00 | 0.10 | 0.00 | 0.00 | 0.12 | 0.05 |
| ADORA2A | ENSG00000128271 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.02 | 0.19 | 0.03 | 0.02 | 0.01 | 0.01 | 0.05 | 0.08 | 0.02 | 0.16 | 0.02 | 0.05 | 0.00 | 0.07 | 0.02 | 0.05 | 0.01 | 0.01 | 0.01 | 0.09 | 0.01 | 0.00 | 0.01 | 0.01 | 0.03 | 0.00 | 0.05 | 0.08 | 0.03 | 0.00 | 0.01 | 0.00 | 0.00 | 0.07 | 0.03 | 0.16 | 0.05 | 0.02 | 0.00 | 0.06 | 0.03 | 0.28 | 0.03 | 0.08 | 0.04 | 0.21 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.00 | 0.05 | 0.00 | 0.00 | 0.06 | 0.03 |
| MCHR1 | ENSG00000128285 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.02 | 0.00 | 0.01 | 0.01 | 0.08 | 0.00 | 0.03 | 0.00 | 0.02 | 0.04 | 0.03 | 0.07 | 0.02 | 0.03 | 0.01 | 0.03 | 0.00 | 0.02 | 0.02 | 0.00 | 0.01 | 0.01 | 0.03 | 0.04 | 0.02 | 0.04 | 0.01 | 0.04 | 0.01 | 0.02 | 0.00 | 0.00 | 0.06 | 0.00 | 0.00 | 0.03 | 0.03 | 0.08 | 0.19 | 0.07 | 0.02 | 0.06 | 0.04 | 0.21 | 0.15 | 0.07 | 0.04 | 0.01 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.05 | 0.00 | 0.00 | 0.28 | 0.00 |
| GALR3 | ENSG00000128310 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.12 | 0.05 | 0.00 | 0.04 | 0.00 | 0.03 | 0.07 | 0.03 | 0.09 | 0.02 | 0.01 | 0.01 | 0.03 | 0.02 | 0.04 | 0.01 | 0.01 | 0.01 | 0.02 | 0.01 | 0.02 | 0.01 | 0.08 | 0.01 | 0.00 | 0.01 | 0.04 | 0.00 | 0.00 | 0.04 | 0.00 | 0.00 | 0.03 | 0.02 | 0.13 | 0.10 | 0.04 | 0.01 | 0.10 | 0.01 | 0.33 | 0.10 | 0.05 | 0.02 | 0.02 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 | 0.01 | 0.04 | 0.02 | 0.00 | 0.14 | 0.01 |
| TST | ENSG00000128311 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.11 | 0.05 | 0.00 | 0.04 | 0.00 | 0.03 | 0.05 | 0.04 | 0.06 | 0.02 | 0.01 | 0.01 | 0.03 | 0.02 | 0.02 | 0.02 | 0.01 | 0.01 | 0.02 | 0.01 | 0.03 | 0.01 | 0.04 | 0.01 | 0.00 | 0.01 | 0.02 | 0.02 | 0.00 | 0.04 | 0.00 | 0.00 | 0.03 | 0.03 | 0.08 | 0.11 | 0.03 | 0.01 | 0.04 | 0.02 | 0.23 | 0.06 | 0.07 | 0.02 | 0.03 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.04 | 0.00 | 0.00 | 0.11 | 0.02 |
| IGLL1 | ENSG00000128322 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.02 | 0.19 | 0.04 | 0.02 | 0.01 | 0.01 | 0.05 | 0.08 | 0.02 | 0.18 | 0.02 | 0.05 | 0.01 | 0.06 | 0.01 | 0.04 | 0.02 | 0.02 | 0.02 | 0.05 | 0.02 | 0.00 | 0.02 | 0.01 | 0.04 | 0.03 | 0.05 | 0.04 | 0.03 | 0.00 | 0.01 | 0.00 | 0.00 | 0.06 | 0.03 | 0.18 | 0.03 | 0.02 | 0.00 | 0.08 | 0.03 | 0.44 | 0.03 | 0.12 | 0.04 | 0.22 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.01 | 0.01 | 0.03 | 0.00 | 0.00 | 0.10 | 0.02 |
| LIF | ENSG00000128342 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.02 | 0.01 | 0.04 | 0.22 | 0.01 | 0.00 | 0.05 | 0.00 | 0.00 | 0.05 | 0.02 | 0.18 | 0.01 | 0.03 | 0.00 | 0.03 | 0.01 | 0.05 | 0.02 | 0.03 | 0.01 | 0.04 | 0.01 | 0.02 | 0.02 | 0.02 | 0.02 | 0.04 | 0.05 | 0.04 | 0.07 | 0.00 | 0.01 | 0.00 | 0.00 | 0.04 | 0.02 | 0.32 | 0.04 | 0.06 | 0.00 | 0.14 | 0.01 | 0.27 | 0.00 | 0.02 | 0.04 | 0.09 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.00 | 0.02 | 0.05 |
| APOBEC3A | ENSG00000128383 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.09 | 0.06 | 0.00 | 0.05 | 0.00 | 0.02 | 0.05 | 0.03 | 0.09 | 0.02 | 0.02 | 0.01 | 0.02 | 0.00 | 0.02 | 0.02 | 0.01 | 0.02 | 0.01 | 0.02 | 0.01 | 0.02 | 0.04 | 0.01 | 0.00 | 0.04 | 0.02 | 0.01 | 0.00 | 0.05 | 0.00 | 0.00 | 0.03 | 0.02 | 0.11 | 0.13 | 0.03 | 0.01 | 0.07 | 0.02 | 0.22 | 0.10 | 0.08 | 0.03 | 0.01 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 | 0.01 | 0.04 | 0.02 | 0.00 | 0.20 | 0.01 |
| CPA4 | ENSG00000128510 | 0.01 | 0.01 | 0.13 | 0.00 | 0.01 | 0.00 | 0.02 | 0.04 | 0.03 | 0.04 | 0.00 | 0.01 | 0.04 | 0.05 | 0.09 | 0.02 | 0.07 | 0.06 | 0.02 | 0.12 | 0.05 | 0.18 | 0.03 | 0.07 | 0.02 | 0.00 | 0.03 | 0.02 | 0.01 | 0.04 | 0.07 | 0.04 | 0.00 | 0.02 | 0.04 | 0.06 | 0.00 | 0.01 | 0.00 | 0.00 | 0.10 | 0.03 | 0.40 | 0.03 | 0.03 | 0.07 | 0.07 | 0.05 | 0.15 | 0.14 | 0.14 | 0.04 | 0.02 | 0.03 | 0.00 | 0.05 | 0.02 | 0.11 | 0.13 | 0.00 | 0.09 | 0.00 | 0.00 | 0.00 | 0.19 | 0.01 |
| TAS2R16 | ENSG00000128519 | 0.01 | 0.01 | 0.11 | 0.00 | 0.01 | 0.00 | 0.02 | 0.03 | 0.04 | 0.04 | 0.00 | 0.01 | 0.04 | 0.07 | 0.07 | 0.02 | 0.08 | 0.06 | 0.03 | 0.10 | 0.03 | 0.17 | 0.06 | 0.06 | 0.02 | 0.00 | 0.00 | 0.02 | 0.01 | 0.04 | 0.08 | 0.04 | 0.00 | 0.02 | 0.00 | 0.06 | 0.00 | 0.02 | 0.00 | 0.00 | 0.06 | 0.04 | 0.28 | 0.06 | 0.04 | 0.06 | 0.01 | 0.05 | 0.05 | 0.12 | 0.19 | 0.03 | 0.03 | 0.02 | 0.00 | 0.03 | 0.09 | 0.07 | 0.10 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.16 | 0.02 |
| VGF | ENSG00000128564 | 0.02 | 0.00 | 0.05 | 0.00 | 0.02 | 0.00 | 0.04 | 0.02 | 0.07 | 0.02 | 0.00 | 0.00 | 0.03 | 0.00 | 0.09 | 0.01 | 0.22 | 0.02 | 0.21 | 0.01 | 0.46 | 0.02 | 0.21 | 0.02 | 0.02 | 0.00 | 0.01 | 0.00 | 0.06 | 0.02 | 0.05 | 0.02 | 0.11 | 0.01 | 0.08 | 0.03 | 0.01 | 0.02 | 0.00 | 0.00 | 0.06 | 0.03 | 0.21 | 0.05 | 0.05 | 0.02 | 0.05 | 0.02 | 0.11 | 0.03 | 0.07 | 0.04 | 0.07 | 0.01 | 0.00 | 0.00 | 0.13 | 0.00 | 0.06 | 0.00 | 0.03 | 0.01 | 0.00 | 0.00 | 0.06 | 0.03 |
| LRRC4 | ENSG00000128594 | 0.01 | 0.01 | 0.08 | 0.01 | 0.01 | 0.00 | 0.02 | 0.05 | 0.04 | 0.05 | 0.00 | 0.01 | 0.04 | 0.07 | 0.06 | 0.02 | 0.06 | 0.08 | 0.03 | 0.13 | 0.04 | 0.21 | 0.04 | 0.09 | 0.03 | 0.01 | 0.03 | 0.02 | 0.01 | 0.04 | 0.03 | 0.06 | 0.00 | 0.07 | 0.01 | 0.06 | 0.00 | 0.02 | 0.00 | 0.00 | 0.08 | 0.04 | 0.34 | 0.06 | 0.02 | 0.07 | 0.03 | 0.05 | 0.05 | 0.18 | 0.14 | 0.03 | 0.03 | 0.04 | 0.00 | 0.06 | 0.02 | 0.11 | 0.11 | 0.00 | 0.06 | 0.00 | 0.00 | 0.00 | 0.18 | 0.01 |
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