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 |
| TYRO3 | ENSG00000092445 | 0.00 | 0.01 | 0.00 | 0.02 | 0.14 | 0.00 | 0.01 | 0.06 | 0.01 | 0.07 | 0.00 | 0.00 | 0.00 | 0.36 | 0.01 | 0.10 | 0.01 | 0.09 | 0.02 | 0.06 | 0.03 | 0.06 | 0.00 | 0.09 | 0.02 | 0.08 | 0.00 | 0.06 | 0.00 | 0.04 | 0.01 | 0.02 | 0.00 | 0.07 | 0.04 | 0.09 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.12 | 0.03 | 0.39 | 0.00 | 0.11 | 0.01 | 0.09 | 0.05 | 0.37 | 0.06 | 0.08 | 0.01 | 0.03 | 0.00 | 0.00 | 0.00 | 0.15 | 0.01 | 0.02 | 0.01 | 0.12 | 0.00 | 0.00 | 0.01 | 0.19 |
| SNAP23 | ENSG00000092531 | 0.00 | 0.01 | 0.00 | 0.02 | 0.14 | 0.00 | 0.01 | 0.06 | 0.01 | 0.08 | 0.00 | 0.00 | 0.02 | 0.34 | 0.00 | 0.10 | 0.01 | 0.09 | 0.02 | 0.05 | 0.03 | 0.06 | 0.01 | 0.08 | 0.01 | 0.10 | 0.00 | 0.06 | 0.00 | 0.04 | 0.00 | 0.03 | 0.00 | 0.07 | 0.02 | 0.08 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.11 | 0.04 | 0.36 | 0.00 | 0.09 | 0.00 | 0.09 | 0.05 | 0.44 | 0.07 | 0.08 | 0.01 | 0.04 | 0.00 | 0.00 | 0.02 | 0.15 | 0.00 | 0.03 | 0.02 | 0.11 | 0.00 | 0.00 | 0.02 | 0.17 |
| TGFB2 | ENSG00000092969 | 0.01 | 0.02 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.07 | 0.10 | 0.06 | 0.02 | 0.02 | 0.05 | 0.01 | 0.08 | 0.01 | 0.11 | 0.01 | 0.04 | 0.00 | 0.20 | 0.04 | 0.06 | 0.01 | 0.02 | 0.01 | 0.06 | 0.02 | 0.00 | 0.01 | 0.13 | 0.02 | 0.16 | 0.02 | 0.04 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.21 | 0.02 | 0.23 | 0.14 | 0.06 | 0.01 | 0.08 | 0.03 | 0.16 | 0.00 | 0.05 | 0.21 | 0.02 | 0.03 | 0.01 | 0.00 | 0.09 | 0.04 | 0.00 | 0.02 | 0.02 | 0.06 | 0.09 | 0.00 | 0.11 | 0.04 |
| COMT | ENSG00000093010 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.05 | 0.17 | 0.06 | 0.03 | 0.01 | 0.08 | 0.05 | 0.07 | 0.03 | 0.17 | 0.07 | 0.10 | 0.03 | 0.08 | 0.07 | 0.05 | 0.04 | 0.02 | 0.01 | 0.06 | 0.03 | 0.00 | 0.02 | 0.02 | 0.03 | 0.08 | 0.10 | 0.10 | 0.14 | 0.01 | 0.01 | 0.02 | 0.00 | 0.06 | 0.05 | 0.19 | 0.07 | 0.05 | 0.01 | 0.06 | 0.06 | 0.42 | 0.04 | 0.14 | 0.07 | 0.13 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 | 0.01 | 0.03 | 0.00 | 0.00 | 0.13 | 0.03 |
| CECR1 | ENSG00000093072 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.04 | 0.14 | 0.06 | 0.02 | 0.00 | 0.07 | 0.05 | 0.06 | 0.04 | 0.15 | 0.07 | 0.06 | 0.04 | 0.05 | 0.13 | 0.05 | 0.04 | 0.01 | 0.02 | 0.06 | 0.04 | 0.00 | 0.02 | 0.02 | 0.02 | 0.08 | 0.10 | 0.09 | 0.07 | 0.00 | 0.01 | 0.02 | 0.00 | 0.06 | 0.06 | 0.13 | 0.10 | 0.04 | 0.01 | 0.07 | 0.06 | 0.25 | 0.07 | 0.14 | 0.06 | 0.10 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.02 | 0.00 | 0.00 | 0.09 | 0.03 |
| HDAC6 | ENSG00000094631 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.04 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.10 | 0.01 | 0.04 | 0.02 | 0.01 | 0.03 | 0.04 | 0.04 | 0.04 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.16 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.06 | 0.01 | 0.47 | 0.07 | 0.04 | 0.03 | 0.11 | 0.01 | 0.19 | 0.03 | 0.11 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.07 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.02 | 0.00 |
| OR1I1 | ENSG00000094661 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.03 | 0.04 | 0.00 | 0.00 | 0.06 | 0.00 | 0.00 | 0.03 | 0.12 | 0.03 | 0.05 | 0.01 | 0.20 | 0.01 | 0.05 | 0.00 | 0.01 | 0.00 | 0.02 | 0.01 | 0.01 | 0.01 | 0.07 | 0.04 | 0.00 | 0.03 | 0.34 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.15 | 0.02 | 0.85 | 0.05 | 0.04 | 0.02 | 0.26 | 0.01 | 0.49 | 0.05 | 0.19 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.02 | 0.00 | 0.02 | 0.00 | 0.02 | 0.00 | 0.04 | 0.01 |
| NXPE1 | ENSG00000095110 | 0.00 | 0.01 | 0.00 | 0.07 | 0.02 | 0.02 | 0.00 | 0.12 | 0.03 | 0.11 | 0.00 | 0.00 | 0.02 | 0.17 | 0.03 | 0.09 | 0.05 | 0.09 | 0.03 | 0.16 | 0.04 | 0.13 | 0.04 | 0.09 | 0.01 | 0.02 | 0.00 | 0.03 | 0.01 | 0.01 | 0.00 | 0.09 | 0.01 | 0.20 | 0.00 | 0.07 | 0.00 | 0.06 | 0.00 | 0.00 | 0.02 | 0.24 | 0.14 | 0.16 | 0.04 | 0.30 | 0.03 | 0.06 | 0.09 | 0.20 | 0.02 | 0.22 | 0.00 | 0.15 | 0.02 | 0.00 | 0.10 | 0.01 | 0.03 | 0.01 | 0.01 | 0.01 | 0.00 | 0.04 | 0.02 | 0.27 |
| CYP26A1 | ENSG00000095596 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.14 | 0.03 | 0.09 | 0.00 | 0.02 | 0.00 | 0.14 | 0.01 | 0.03 | 0.04 | 0.07 | 0.01 | 0.06 | 0.02 | 0.10 | 0.01 | 0.10 | 0.01 | 0.09 | 0.00 | 0.07 | 0.01 | 0.02 | 0.01 | 0.06 | 0.16 | 0.07 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.01 | 0.01 | 0.08 | 0.07 | 0.32 | 0.01 | 0.06 | 0.03 | 0.10 | 0.05 | 0.09 | 0.01 | 0.06 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.07 | 0.01 | 0.04 | 0.01 | 0.05 | 0.00 | 0.00 | 0.01 | 0.03 |
| TDRD1 | ENSG00000095627 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.05 | 0.02 | 0.09 | 0.00 | 0.02 | 0.01 | 0.17 | 0.06 | 0.03 | 0.04 | 0.06 | 0.01 | 0.03 | 0.03 | 0.06 | 0.08 | 0.05 | 0.01 | 0.06 | 0.01 | 0.06 | 0.01 | 0.01 | 0.01 | 0.10 | 0.11 | 0.25 | 0.09 | 0.00 | 0.01 | 0.02 | 0.00 | 0.00 | 0.04 | 0.09 | 0.19 | 0.22 | 0.01 | 0.06 | 0.03 | 0.06 | 0.04 | 0.05 | 0.04 | 0.06 | 0.07 | 0.00 | 0.00 | 0.00 | 0.00 | 0.10 | 0.00 | 0.11 | 0.00 | 0.06 | 0.00 | 0.00 | 0.01 | 0.05 |
| IL11 | ENSG00000095752 | 0.01 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.03 | 0.00 | 0.20 | 0.03 | 0.00 | 0.00 | 0.01 | 0.04 | 0.05 | 0.05 | 0.12 | 0.08 | 0.05 | 0.02 | 0.15 | 0.03 | 0.13 | 0.02 | 0.03 | 0.03 | 0.01 | 0.04 | 0.05 | 0.04 | 0.06 | 0.02 | 0.02 | 0.07 | 0.21 | 0.00 | 0.00 | 0.03 | 0.00 | 0.00 | 0.17 | 0.03 | 0.16 | 0.27 | 0.14 | 0.06 | 0.06 | 0.05 | 0.42 | 0.10 | 0.04 | 0.19 | 0.00 | 0.06 | 0.01 | 0.00 | 0.26 | 0.03 | 0.00 | 0.19 | 0.03 | 0.12 | 0.00 | 0.00 | 0.03 | 0.05 |
| MYO3A | ENSG00000095777 | 0.00 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 | 0.05 | 0.04 | 0.00 | 0.01 | 0.02 | 0.00 | 0.04 | 0.02 | 0.03 | 0.02 | 0.04 | 0.02 | 0.06 | 0.02 | 0.04 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.01 | 0.03 | 0.07 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.03 | 0.10 | 0.06 | 0.01 | 0.01 | 0.02 | 0.02 | 0.08 | 0.00 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.01 | 0.02 | 0.00 | 0.00 | 0.03 | 0.01 |
| TPSD1 | ENSG00000095917 | 0.01 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.02 | 0.15 | 0.00 | 0.00 | 0.04 | 0.02 | 0.05 | 0.05 | 0.04 | 0.09 | 0.03 | 0.03 | 0.03 | 0.12 | 0.04 | 0.08 | 0.03 | 0.04 | 0.03 | 0.03 | 0.01 | 0.02 | 0.03 | 0.06 | 0.00 | 0.05 | 0.17 | 0.01 | 0.00 | 0.02 | 0.00 | 0.00 | 0.09 | 0.02 | 0.11 | 0.19 | 0.10 | 0.05 | 0.03 | 0.04 | 0.17 | 0.21 | 0.09 | 0.05 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.04 | 0.01 | 0.00 | 0.02 | 0.02 | 0.00 | 0.00 | 0.05 | 0.02 |
| KCNK16 | ENSG00000095981 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.11 | 0.03 | 0.00 | 0.00 | 0.02 | 0.02 | 0.11 | 0.01 | 0.09 | 0.05 | 0.03 | 0.02 | 0.25 | 0.03 | 0.13 | 0.02 | 0.05 | 0.01 | 0.07 | 0.00 | 0.03 | 0.01 | 0.06 | 0.00 | 0.05 | 0.03 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.10 | 0.03 | 0.29 | 0.05 | 0.05 | 0.01 | 0.04 | 0.01 | 0.16 | 0.03 | 0.11 | 0.05 | 0.05 | 0.01 | 0.00 | 0.00 | 0.14 | 0.00 | 0.02 | 0.00 | 0.02 | 0.01 | 0.09 | 0.00 | 0.06 | 0.00 |
| NCR2 | ENSG00000096264 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.15 | 0.03 | 0.01 | 0.00 | 0.02 | 0.03 | 0.14 | 0.01 | 0.10 | 0.06 | 0.05 | 0.02 | 0.43 | 0.02 | 0.27 | 0.01 | 0.10 | 0.00 | 0.12 | 0.00 | 0.04 | 0.00 | 0.07 | 0.00 | 0.05 | 0.03 | 0.07 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.11 | 0.03 | 0.30 | 0.05 | 0.05 | 0.02 | 0.05 | 0.01 | 0.06 | 0.03 | 0.24 | 0.03 | 0.05 | 0.01 | 0.00 | 0.00 | 0.14 | 0.00 | 0.01 | 0.00 | 0.01 | 0.01 | 0.04 | 0.00 | 0.04 | 0.00 |
| MLN | ENSG00000096395 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.06 | 0.05 | 0.00 | 0.01 | 0.03 | 0.01 | 0.08 | 0.01 | 0.03 | 0.06 | 0.02 | 0.03 | 0.15 | 0.06 | 0.06 | 0.03 | 0.03 | 0.01 | 0.06 | 0.02 | 0.04 | 0.02 | 0.06 | 0.01 | 0.05 | 0.03 | 0.05 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.08 | 0.02 | 0.26 | 0.05 | 0.09 | 0.01 | 0.05 | 0.01 | 0.05 | 0.01 | 0.06 | 0.07 | 0.00 | 0.01 | 0.00 | 0.00 | 0.08 | 0.03 | 0.01 | 0.00 | 0.01 | 0.01 | 0.10 | 0.00 | 0.10 | 0.01 |
| CDC7 | ENSG00000097046 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.07 | 0.05 | 0.07 | 0.00 | 0.00 | 0.00 | 0.39 | 0.04 | 0.09 | 0.05 | 0.06 | 0.01 | 0.08 | 0.00 | 0.09 | 0.01 | 0.07 | 0.00 | 0.07 | 0.01 | 0.05 | 0.00 | 0.01 | 0.03 | 0.03 | 0.00 | 0.10 | 0.02 | 0.05 | 0.00 | 0.22 | 0.00 | 0.00 | 0.06 | 0.11 | 0.16 | 0.18 | 0.00 | 0.04 | 0.01 | 0.03 | 0.05 | 0.06 | 0.11 | 0.08 | 0.04 | 0.06 | 0.01 | 0.00 | 0.00 | 0.03 | 0.01 | 0.01 | 0.01 | 0.06 | 0.00 | 0.05 | 0.04 | 0.12 |
| TMED1 | ENSG00000099203 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.02 | 0.10 | 0.05 | 0.00 | 0.01 | 0.09 | 0.01 | 0.01 | 0.05 | 0.08 | 0.06 | 0.05 | 0.03 | 0.08 | 0.06 | 0.04 | 0.04 | 0.02 | 0.02 | 0.03 | 0.02 | 0.01 | 0.03 | 0.01 | 0.11 | 0.00 | 0.01 | 0.15 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.09 | 0.04 | 0.56 | 0.19 | 0.13 | 0.05 | 0.26 | 0.05 | 0.64 | 0.12 | 0.26 | 0.02 | 0.02 | 0.00 | 0.03 | 0.00 | 0.00 | 0.06 | 0.01 | 0.00 | 0.04 | 0.00 | 0.07 | 0.02 | 0.03 | 0.02 |
| PRTFDC1 | ENSG00000099256 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 | 0.03 | 0.05 | 0.00 | 0.01 | 0.02 | 0.00 | 0.03 | 0.02 | 0.02 | 0.03 | 0.03 | 0.02 | 0.06 | 0.03 | 0.05 | 0.03 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.02 | 0.07 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.02 | 0.11 | 0.07 | 0.01 | 0.01 | 0.02 | 0.02 | 0.08 | 0.00 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.04 | 0.04 | 0.01 | 0.02 | 0.01 | 0.01 | 0.00 | 0.00 | 0.02 | 0.03 |
| KCNK6 | ENSG00000099337 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.02 | 0.02 | 0.01 | 0.34 | 0.01 | 0.00 | 0.00 | 0.08 | 0.02 | 0.19 | 0.03 | 0.57 | 0.03 | 0.07 | 0.01 | 0.15 | 0.03 | 0.10 | 0.02 | 0.04 | 0.01 | 0.01 | 0.01 | 0.19 | 0.00 | 0.03 | 0.01 | 0.12 | 0.03 | 0.06 | 0.03 | 0.01 | 0.02 | 0.00 | 0.00 | 0.17 | 0.02 | 0.72 | 0.11 | 0.29 | 0.03 | 0.17 | 0.03 | 1.14 | 0.09 | 0.23 | 0.09 | 0.00 | 0.03 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.04 | 0.04 | 0.03 | 0.00 | 0.00 | 0.05 | 0.01 |
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