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 |
| LAG3 | ENSG00000089692 | 0.01 | 0.00 | 0.00 | 0.01 | 0.02 | 0.00 | 0.01 | 0.07 | 0.09 | 0.02 | 0.01 | 0.00 | 0.00 | 0.08 | 0.07 | 0.07 | 0.17 | 0.01 | 0.11 | 0.01 | 0.08 | 0.02 | 0.06 | 0.05 | 0.05 | 0.02 | 0.05 | 0.03 | 0.05 | 0.05 | 0.03 | 0.04 | 0.18 | 0.05 | 0.06 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.13 | 0.04 | 0.35 | 0.07 | 0.03 | 0.02 | 0.09 | 0.02 | 0.08 | 0.03 | 0.08 | 0.11 | 0.60 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.15 | 0.01 | 0.05 | 0.01 | 0.00 | 0.01 | 0.04 | 0.04 |
| LTBP4 | ENSG00000090006 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.02 | 0.01 | 0.03 | 0.19 | 0.02 | 0.00 | 0.00 | 0.08 | 0.02 | 0.15 | 0.04 | 0.34 | 0.06 | 0.05 | 0.02 | 0.03 | 0.05 | 0.08 | 0.03 | 0.05 | 0.01 | 0.01 | 0.01 | 0.18 | 0.01 | 0.08 | 0.02 | 0.12 | 0.01 | 0.11 | 0.04 | 0.00 | 0.02 | 0.00 | 0.00 | 0.09 | 0.04 | 0.38 | 0.24 | 0.10 | 0.04 | 0.12 | 0.04 | 0.91 | 0.11 | 0.21 | 0.12 | 0.00 | 0.03 | 0.01 | 0.00 | 0.05 | 0.00 | 0.02 | 0.06 | 0.02 | 0.07 | 0.00 | 0.00 | 0.02 | 0.01 |
| LYZ | ENSG00000090382 | 0.00 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.04 | 0.00 | 0.60 | 0.01 | 0.00 | 0.00 | 0.03 | 0.00 | 0.33 | 0.01 | 0.27 | 0.01 | 0.28 | 0.01 | 0.49 | 0.01 | 0.46 | 0.01 | 0.01 | 0.01 | 0.05 | 0.03 | 0.11 | 0.02 | 0.08 | 0.00 | 0.26 | 0.01 | 0.33 | 0.02 | 0.05 | 0.01 | 0.00 | 0.00 | 0.32 | 0.01 | 0.31 | 0.04 | 0.09 | 0.00 | 0.05 | 0.01 | 0.51 | 0.07 | 1.50 | 0.04 | 0.26 | 0.00 | 0.00 | 0.01 | 0.11 | 0.00 | 0.04 | 0.02 | 0.22 | 0.04 | 0.02 | 0.00 | 0.27 | 0.01 |
| SI | ENSG00000090402 | 0.05 | 0.00 | 0.03 | 0.01 | 0.00 | 0.00 | 0.06 | 0.01 | 0.15 | 0.01 | 0.00 | 0.00 | 0.00 | 0.06 | 0.14 | 0.01 | 1.34 | 0.00 | 0.52 | 0.00 | 0.74 | 0.00 | 0.21 | 0.01 | 0.03 | 0.02 | 0.04 | 0.00 | 0.03 | 0.00 | 0.09 | 0.01 | 0.08 | 0.01 | 0.10 | 0.00 | 0.00 | 0.06 | 0.00 | 0.00 | 0.18 | 0.02 | 1.00 | 0.02 | 0.62 | 0.01 | 0.23 | 0.01 | 0.35 | 0.00 | 0.06 | 0.09 | 0.18 | 0.00 | 0.00 | 0.00 | 0.04 | 0.00 | 0.02 | 0.00 | 0.04 | 0.02 | 0.00 | 0.00 | 0.02 | 0.03 |
| DNAJB11 | ENSG00000090520 | 0.05 | 0.00 | 0.03 | 0.01 | 0.00 | 0.01 | 0.03 | 0.04 | 0.19 | 0.01 | 0.00 | 0.00 | 0.00 | 0.07 | 0.14 | 0.05 | 1.59 | 0.00 | 0.61 | 0.00 | 0.70 | 0.02 | 0.21 | 0.01 | 0.04 | 0.01 | 0.06 | 0.02 | 0.03 | 0.00 | 0.14 | 0.02 | 0.12 | 0.03 | 0.10 | 0.00 | 0.00 | 0.10 | 0.00 | 0.00 | 0.18 | 0.02 | 1.07 | 0.04 | 0.62 | 0.00 | 0.33 | 0.01 | 0.78 | 0.09 | 0.12 | 0.09 | 0.24 | 0.00 | 0.00 | 0.00 | 0.06 | 0.00 | 0.02 | 0.02 | 0.13 | 0.05 | 0.00 | 0.00 | 0.03 | 0.04 |
| THPO | ENSG00000090534 | 0.05 | 0.00 | 0.03 | 0.01 | 0.00 | 0.01 | 0.03 | 0.03 | 0.17 | 0.00 | 0.00 | 0.00 | 0.00 | 0.08 | 0.15 | 0.05 | 1.85 | 0.00 | 0.65 | 0.00 | 0.72 | 0.02 | 0.23 | 0.01 | 0.04 | 0.00 | 0.06 | 0.03 | 0.03 | 0.01 | 0.11 | 0.02 | 0.12 | 0.01 | 0.10 | 0.00 | 0.00 | 0.10 | 0.00 | 0.00 | 0.19 | 0.02 | 1.12 | 0.02 | 0.62 | 0.00 | 0.35 | 0.01 | 0.76 | 0.09 | 0.12 | 0.10 | 0.22 | 0.00 | 0.00 | 0.01 | 0.06 | 0.00 | 0.06 | 0.00 | 0.20 | 0.02 | 0.00 | 0.00 | 0.03 | 0.05 |
| CD209 | ENSG00000090659 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.02 | 0.01 | 0.03 | 0.07 | 0.08 | 0.00 | 0.01 | 0.01 | 0.07 | 0.01 | 0.05 | 0.05 | 0.09 | 0.02 | 0.08 | 0.01 | 0.10 | 0.02 | 0.07 | 0.01 | 0.02 | 0.00 | 0.04 | 0.00 | 0.04 | 0.00 | 0.11 | 0.00 | 0.01 | 0.07 | 0.03 | 0.01 | 0.00 | 0.00 | 0.01 | 0.07 | 0.08 | 0.26 | 0.44 | 0.04 | 0.14 | 0.05 | 0.19 | 0.10 | 0.56 | 0.27 | 0.01 | 0.02 | 0.00 | 0.04 | 0.00 | 0.00 | 0.09 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.05 | 0.05 | 0.03 |
| EFNB1 | ENSG00000090776 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.02 | 0.00 | 0.06 | 0.05 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.02 | 0.04 | 0.04 | 0.05 | 0.02 | 0.13 | 0.02 | 0.02 | 0.02 | 0.01 | 0.01 | 0.00 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.07 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.02 | 0.18 | 0.04 | 0.03 | 0.01 | 0.05 | 0.01 | 0.20 | 0.00 | 0.17 | 0.06 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 | 0.03 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.02 | 0.01 |
| SLC26A4 | ENSG00000091137 | 0.01 | 0.00 | 0.07 | 0.01 | 0.01 | 0.00 | 0.04 | 0.03 | 0.05 | 0.02 | 0.00 | 0.00 | 0.03 | 0.02 | 0.10 | 0.02 | 0.14 | 0.03 | 0.16 | 0.03 | 0.35 | 0.07 | 0.10 | 0.04 | 0.02 | 0.00 | 0.01 | 0.00 | 0.03 | 0.03 | 0.07 | 0.02 | 0.00 | 0.02 | 0.02 | 0.06 | 0.00 | 0.02 | 0.00 | 0.00 | 0.06 | 0.04 | 0.25 | 0.06 | 0.04 | 0.02 | 0.03 | 0.03 | 0.12 | 0.05 | 0.16 | 0.02 | 0.08 | 0.01 | 0.00 | 0.02 | 0.13 | 0.00 | 0.09 | 0.00 | 0.02 | 0.01 | 0.00 | 0.00 | 0.08 | 0.03 |
| SLC26A3 | ENSG00000091138 | 0.01 | 0.00 | 0.05 | 0.01 | 0.01 | 0.00 | 0.04 | 0.03 | 0.05 | 0.02 | 0.00 | 0.00 | 0.03 | 0.02 | 0.09 | 0.02 | 0.14 | 0.03 | 0.16 | 0.02 | 0.33 | 0.07 | 0.08 | 0.04 | 0.01 | 0.01 | 0.01 | 0.00 | 0.03 | 0.02 | 0.07 | 0.02 | 0.00 | 0.02 | 0.02 | 0.06 | 0.00 | 0.02 | 0.00 | 0.00 | 0.06 | 0.04 | 0.26 | 0.06 | 0.04 | 0.04 | 0.04 | 0.03 | 0.12 | 0.05 | 0.21 | 0.02 | 0.08 | 0.01 | 0.00 | 0.02 | 0.13 | 0.00 | 0.10 | 0.00 | 0.02 | 0.01 | 0.00 | 0.00 | 0.08 | 0.03 |
| TXNL1 | ENSG00000091164 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.07 | 0.03 | 0.08 | 0.00 | 0.00 | 0.00 | 0.07 | 0.01 | 0.10 | 0.03 | 0.07 | 0.01 | 0.13 | 0.02 | 0.21 | 0.01 | 0.18 | 0.00 | 0.10 | 0.00 | 0.10 | 0.00 | 0.08 | 0.02 | 0.07 | 0.00 | 0.10 | 0.00 | 0.05 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.06 | 0.03 | 0.32 | 0.02 | 0.04 | 0.02 | 0.07 | 0.01 | 0.09 | 0.10 | 0.08 | 0.01 | 0.05 | 0.00 | 0.01 | 0.12 | 0.00 | 0.02 | 0.03 | 0.00 | 0.03 | 0.00 | 0.01 | 0.03 | 0.03 |
| IL5RA | ENSG00000091181 | 0.00 | 0.17 | 0.00 | 0.01 | 0.07 | 0.00 | 0.02 | 0.04 | 0.22 | 0.06 | 0.00 | 0.06 | 0.04 | 0.11 | 0.03 | 0.05 | 0.03 | 0.07 | 0.03 | 0.03 | 0.03 | 0.10 | 0.03 | 0.11 | 0.01 | 0.05 | 0.01 | 0.06 | 0.01 | 0.02 | 0.05 | 0.03 | 0.00 | 0.18 | 0.09 | 0.01 | 0.00 | 0.04 | 0.00 | 0.00 | 0.12 | 0.04 | 0.13 | 0.26 | 0.04 | 0.02 | 0.04 | 0.04 | 0.05 | 0.22 | 0.22 | 0.06 | 0.05 | 0.07 | 0.01 | 0.00 | 0.00 | 0.05 | 0.03 | 0.02 | 0.01 | 0.02 | 0.00 | 0.00 | 0.02 | 0.06 |
| pk | ENSG00000091436 | 0.02 | 0.00 | 0.07 | 0.00 | 0.00 | 0.00 | 0.01 | 0.09 | 0.07 | 0.04 | 0.00 | 0.01 | 0.00 | 0.00 | 0.05 | 0.01 | 0.15 | 0.01 | 0.17 | 0.01 | 0.22 | 0.03 | 0.06 | 0.04 | 0.01 | 0.01 | 0.03 | 0.02 | 0.06 | 0.01 | 0.09 | 0.04 | 0.05 | 0.01 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.04 | 0.38 | 0.03 | 0.11 | 0.01 | 0.07 | 0.01 | 0.11 | 0.00 | 0.03 | 0.10 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.01 |
| SLC17A6 | ENSG00000091664 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.04 | 0.00 | 0.00 | 0.04 | 0.09 | 0.00 | 0.00 | 0.00 | 0.03 | 0.03 | 0.02 | 0.05 | 0.05 | 0.01 | 0.04 | 0.05 | 0.03 | 0.02 | 0.02 | 0.02 | 0.01 | 0.02 | 0.04 | 0.00 | 0.02 | 0.03 | 0.01 | 0.00 | 0.01 | 0.02 | 0.02 | 0.04 | 0.04 | 0.00 | 0.00 | 0.07 | 0.04 | 0.07 | 0.18 | 0.01 | 0.04 | 0.01 | 0.03 | 0.01 | 0.02 | 0.04 | 0.06 | 0.01 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 | 0.02 | 0.00 | 0.00 | 0.02 | 0.01 |
| ANGPT2 | ENSG00000091879 | 0.00 | 0.02 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.09 | 0.02 | 0.14 | 0.00 | 0.00 | 0.04 | 0.04 | 0.04 | 0.07 | 0.01 | 0.13 | 0.00 | 0.08 | 0.16 | 0.07 | 0.12 | 0.04 | 0.02 | 0.10 | 0.00 | 0.19 | 0.03 | 0.04 | 0.01 | 0.13 | 0.00 | 0.01 | 0.00 | 0.05 | 0.00 | 0.02 | 0.00 | 0.00 | 0.03 | 0.15 | 0.04 | 0.41 | 0.01 | 0.07 | 0.01 | 0.09 | 0.03 | 0.27 | 0.07 | 0.13 | 0.02 | 0.01 | 0.00 | 0.00 | 0.04 | 0.09 | 0.00 | 0.01 | 0.01 | 0.02 | 0.00 | 0.01 | 0.01 | 0.03 |
| CD200 | ENSG00000091972 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.04 | 0.05 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.04 | 0.02 | 0.13 | 0.03 | 0.05 | 0.01 | 0.08 | 0.05 | 0.06 | 0.02 | 0.00 | 0.00 | 0.01 | 0.02 | 0.00 | 0.00 | 0.02 | 0.01 | 0.00 | 0.01 | 0.10 | 0.02 | 0.00 | 0.05 | 0.00 | 0.00 | 0.06 | 0.02 | 0.40 | 0.04 | 0.05 | 0.01 | 0.04 | 0.01 | 0.03 | 0.08 | 0.10 | 0.04 | 0.01 | 0.01 | 0.00 | 0.00 | 0.04 | 0.02 | 0.00 | 0.03 | 0.01 | 0.05 | 0.00 | 0.00 | 0.02 | 0.04 |
| CMA1 | ENSG00000092009 | 0.00 | 0.00 | 0.03 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.08 | 0.07 | 0.00 | 0.00 | 0.00 | 0.02 | 0.16 | 0.02 | 0.10 | 0.07 | 0.05 | 0.07 | 0.13 | 0.04 | 0.05 | 0.04 | 0.02 | 0.02 | 0.01 | 0.06 | 0.00 | 0.03 | 0.07 | 0.01 | 0.00 | 0.02 | 0.26 | 0.03 | 0.00 | 0.01 | 0.00 | 0.00 | 0.10 | 0.04 | 0.18 | 0.12 | 0.03 | 0.02 | 0.05 | 0.03 | 0.06 | 0.07 | 0.20 | 0.03 | 0.01 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.03 | 0.03 | 0.01 | 0.09 | 0.00 | 0.00 | 0.03 | 0.03 |
| MYH7 | ENSG00000092054 | 0.00 | 0.00 | 0.03 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.14 | 0.07 | 0.01 | 0.00 | 0.00 | 0.02 | 0.19 | 0.03 | 0.16 | 0.07 | 0.06 | 0.07 | 0.12 | 0.05 | 0.05 | 0.04 | 0.03 | 0.03 | 0.01 | 0.07 | 0.01 | 0.03 | 0.08 | 0.00 | 0.00 | 0.02 | 0.28 | 0.03 | 0.00 | 0.02 | 0.00 | 0.00 | 0.12 | 0.03 | 0.26 | 0.12 | 0.07 | 0.02 | 0.05 | 0.03 | 0.06 | 0.07 | 0.23 | 0.03 | 0.01 | 0.03 | 0.00 | 0.01 | 0.00 | 0.00 | 0.03 | 0.03 | 0.02 | 0.09 | 0.00 | 0.02 | 0.03 | 0.03 |
| OSGEP | ENSG00000092094 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.02 | 0.08 | 0.05 | 0.00 | 0.00 | 0.00 | 0.05 | 0.16 | 0.04 | 0.18 | 0.07 | 0.08 | 0.06 | 0.12 | 0.07 | 0.08 | 0.04 | 0.03 | 0.02 | 0.01 | 0.10 | 0.01 | 0.04 | 0.09 | 0.00 | 0.00 | 0.02 | 0.18 | 0.03 | 0.01 | 0.02 | 0.00 | 0.00 | 0.09 | 0.04 | 0.41 | 0.10 | 0.07 | 0.02 | 0.08 | 0.03 | 0.15 | 0.08 | 0.18 | 0.09 | 0.02 | 0.01 | 0.00 | 0.01 | 0.01 | 0.00 | 0.02 | 0.02 | 0.01 | 0.10 | 0.00 | 0.00 | 0.03 | 0.02 |
| TGM1 | ENSG00000092295 | 0.00 | 0.00 | 0.03 | 0.01 | 0.00 | 0.00 | 0.01 | 0.01 | 0.09 | 0.06 | 0.01 | 0.00 | 0.00 | 0.02 | 0.15 | 0.03 | 0.10 | 0.07 | 0.05 | 0.07 | 0.11 | 0.05 | 0.05 | 0.04 | 0.02 | 0.02 | 0.01 | 0.06 | 0.00 | 0.03 | 0.08 | 0.01 | 0.00 | 0.02 | 0.28 | 0.03 | 0.00 | 0.02 | 0.00 | 0.00 | 0.10 | 0.04 | 0.17 | 0.13 | 0.03 | 0.03 | 0.05 | 0.03 | 0.27 | 0.12 | 0.22 | 0.03 | 0.01 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.03 | 0.03 | 0.00 | 0.09 | 0.00 | 0.00 | 0.03 | 0.03 |
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