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 |
| HSD11B1L | ENSG00000167733 | 0.00 | 0.01 | 0.00 | 0.02 | 0.00 | 0.04 | 0.01 | 0.03 | 0.03 | 0.10 | 0.00 | 0.03 | 0.01 | 0.09 | 0.01 | 0.06 | 0.05 | 0.09 | 0.05 | 0.10 | 0.04 | 0.11 | 0.02 | 0.07 | 0.02 | 0.03 | 0.01 | 0.08 | 0.00 | 0.06 | 0.01 | 0.12 | 0.00 | 0.01 | 0.01 | 0.03 | 0.01 | 0.00 | 0.00 | 0.00 | 0.06 | 0.08 | 0.11 | 0.64 | 0.03 | 0.18 | 0.01 | 0.23 | 0.02 | 0.56 | 0.22 | 0.05 | 0.02 | 0.00 | 0.00 | 0.01 | 0.00 | 0.03 | 0.01 | 0.01 | 0.04 | 0.01 | 0.00 | 0.05 | 0.05 | 0.04 |
| SLCO1A2 | ENSG00000084453 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.02 | 0.06 | 0.07 | 0.04 | 0.01 | 0.00 | 0.00 | 0.04 | 0.18 | 0.05 | 0.17 | 0.01 | 0.08 | 0.01 | 0.14 | 0.01 | 0.13 | 0.04 | 0.02 | 0.01 | 0.13 | 0.03 | 0.09 | 0.04 | 0.00 | 0.04 | 0.14 | 0.07 | 0.05 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.08 | 0.04 | 0.32 | 0.06 | 0.01 | 0.02 | 0.05 | 0.01 | 0.17 | 0.03 | 0.14 | 0.09 | 0.62 | 0.00 | 0.00 | 0.01 | 0.00 | 0.04 | 0.07 | 0.01 | 0.05 | 0.04 | 0.00 | 0.01 | 0.05 | 0.01 |
| TXNDC16 | ENSG00000087301 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.02 | 0.03 | 0.00 | 0.01 | 0.00 | 0.05 | 0.13 | 0.01 | 0.07 | 0.04 | 0.07 | 0.02 | 0.13 | 0.01 | 0.06 | 0.02 | 0.00 | 0.01 | 0.01 | 0.02 | 0.02 | 0.01 | 0.03 | 0.05 | 0.05 | 0.06 | 0.04 | 0.05 | 0.01 | 0.01 | 0.00 | 0.00 | 0.10 | 0.02 | 0.09 | 0.13 | 0.01 | 0.02 | 0.02 | 0.01 | 0.00 | 0.07 | 0.06 | 0.09 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.00 | 0.01 | 0.03 | 0.00 | 0.04 | 0.00 | 0.00 | 0.02 | 0.02 |
| SLC16A6 | ENSG00000108932 | 0.02 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.03 | 0.02 | 0.21 | 0.01 | 0.05 | 0.00 | 0.12 | 0.00 | 0.16 | 0.00 | 0.21 | 0.01 | 0.07 | 0.02 | 0.21 | 0.03 | 0.12 | 0.04 | 0.08 | 0.01 | 0.09 | 0.02 | 0.05 | 0.10 | 0.22 | 0.01 | 0.12 | 0.01 | 0.15 | 0.16 | 0.02 | 0.01 | 0.00 | 0.00 | 0.56 | 0.01 | 0.26 | 0.04 | 0.16 | 0.03 | 0.13 | 0.01 | 0.45 | 0.02 | 0.22 | 0.04 | 0.03 | 0.00 | 0.01 | 0.00 | 0.05 | 0.00 | 0.07 | 0.00 | 0.03 | 0.00 | 0.17 | 0.01 | 0.23 | 0.02 |
| OXNAD1 | ENSG00000154814 | 0.00 | 0.18 | 0.00 | 0.01 | 0.07 | 0.00 | 0.00 | 0.02 | 0.24 | 0.02 | 0.00 | 0.03 | 0.01 | 0.03 | 0.03 | 0.05 | 0.01 | 0.04 | 0.01 | 0.02 | 0.02 | 0.03 | 0.05 | 0.04 | 0.01 | 0.03 | 0.03 | 0.05 | 0.01 | 0.02 | 0.06 | 0.01 | 0.00 | 0.18 | 0.06 | 0.01 | 0.00 | 0.04 | 0.00 | 0.00 | 0.12 | 0.03 | 0.13 | 0.21 | 0.01 | 0.02 | 0.04 | 0.04 | 0.05 | 0.11 | 0.19 | 0.02 | 0.05 | 0.04 | 0.00 | 0.00 | 0.00 | 0.08 | 0.03 | 0.01 | 0.00 | 0.02 | 0.00 | 0.00 | 0.03 | 0.05 |
| CYB5R2 | ENSG00000166394 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 | 0.02 | 0.00 | 0.10 | 0.00 | 0.00 | 0.02 | 0.07 | 0.01 | 0.06 | 0.02 | 0.13 | 0.01 | 0.06 | 0.05 | 0.08 | 0.02 | 0.04 | 0.01 | 0.01 | 0.01 | 0.02 | 0.00 | 0.05 | 0.03 | 0.02 | 0.03 | 0.01 | 0.01 | 0.04 | 0.02 | 0.07 | 0.00 | 0.00 | 0.04 | 0.09 | 0.01 | 0.40 | 0.01 | 0.06 | 0.02 | 0.07 | 0.10 | 0.05 | 0.08 | 0.11 | 0.02 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.01 | 0.08 | 0.00 | 0.04 | 0.00 | 0.00 | 0.02 | 0.02 |
| ADAM28 | ENSG00000042980 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.22 | 0.01 | 0.12 | 0.00 | 0.00 | 0.00 | 0.08 | 0.01 | 0.07 | 0.00 | 0.11 | 0.00 | 0.06 | 0.02 | 0.06 | 0.02 | 0.05 | 0.00 | 0.11 | 0.01 | 0.17 | 0.00 | 0.04 | 0.00 | 0.11 | 0.00 | 0.08 | 0.02 | 0.00 | 0.02 | 0.02 | 0.00 | 0.00 | 0.02 | 0.16 | 0.01 | 0.45 | 0.00 | 0.04 | 0.01 | 0.12 | 0.00 | 0.24 | 0.02 | 0.07 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.11 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.01 | 0.02 | 0.05 |
| LMTK2 | ENSG00000164715 | 0.01 | 0.00 | 0.05 | 0.00 | 0.00 | 0.00 | 0.06 | 0.01 | 0.07 | 0.01 | 0.00 | 0.00 | 0.03 | 0.00 | 0.12 | 0.01 | 0.21 | 0.01 | 0.24 | 0.00 | 0.64 | 0.02 | 0.38 | 0.01 | 0.03 | 0.00 | 0.01 | 0.00 | 0.15 | 0.02 | 0.09 | 0.02 | 0.11 | 0.01 | 0.10 | 0.03 | 0.00 | 0.02 | 0.00 | 0.00 | 0.06 | 0.03 | 0.18 | 0.06 | 0.05 | 0.01 | 0.05 | 0.01 | 0.08 | 0.04 | 0.09 | 0.03 | 0.11 | 0.00 | 0.00 | 0.00 | 0.13 | 0.00 | 0.05 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.05 | 0.02 |
| MAPK4 | ENSG00000141639 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.00 | 0.07 | 0.00 | 0.00 | 0.00 | 0.05 | 0.00 | 0.11 | 0.01 | 0.04 | 0.01 | 0.09 | 0.02 | 0.26 | 0.02 | 0.19 | 0.01 | 0.11 | 0.00 | 0.13 | 0.01 | 0.15 | 0.01 | 0.07 | 0.00 | 0.05 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.07 | 0.06 | 0.26 | 0.01 | 0.04 | 0.02 | 0.06 | 0.01 | 0.07 | 0.07 | 0.06 | 0.01 | 0.03 | 0.00 | 0.01 | 0.05 | 0.00 | 0.00 | 0.02 | 0.00 | 0.03 | 0.00 | 0.01 | 0.02 | 0.01 |
| GPI | ENSG00000105220 | 0.00 | 0.00 | 0.03 | 0.00 | 0.00 | 0.02 | 0.02 | 0.01 | 0.21 | 0.02 | 0.00 | 0.00 | 0.07 | 0.01 | 0.24 | 0.01 | 0.37 | 0.03 | 0.05 | 0.02 | 0.19 | 0.05 | 0.13 | 0.05 | 0.05 | 0.01 | 0.04 | 0.00 | 0.10 | 0.00 | 0.05 | 0.02 | 0.13 | 0.03 | 0.00 | 0.03 | 0.00 | 0.02 | 0.00 | 0.00 | 0.13 | 0.02 | 0.64 | 0.05 | 0.11 | 0.02 | 0.19 | 0.02 | 1.39 | 0.00 | 0.25 | 0.03 | 0.02 | 0.02 | 0.00 | 0.01 | 0.08 | 0.00 | 0.02 | 0.01 | 0.03 | 0.02 | 0.00 | 0.00 | 0.06 | 0.01 |
| INPP5B | ENSG00000204084 | 0.00 | 0.03 | 0.01 | 0.04 | 0.00 | 0.00 | 0.00 | 0.01 | 0.12 | 0.04 | 0.00 | 0.00 | 0.11 | 0.05 | 0.08 | 0.03 | 0.09 | 0.04 | 0.06 | 0.02 | 0.16 | 0.03 | 0.06 | 0.03 | 0.03 | 0.03 | 0.01 | 0.04 | 0.05 | 0.01 | 0.02 | 0.11 | 0.00 | 0.26 | 0.01 | 0.03 | 0.03 | 0.07 | 0.00 | 0.00 | 0.08 | 0.05 | 0.58 | 0.08 | 0.05 | 0.01 | 0.08 | 0.03 | 0.05 | 0.04 | 0.10 | 0.03 | 0.09 | 0.03 | 0.02 | 0.00 | 0.00 | 0.07 | 0.00 | 0.01 | 0.03 | 0.02 | 0.00 | 0.10 | 0.04 | 0.03 |
| FBLN2 | ENSG00000163520 | 0.00 | 0.18 | 0.00 | 0.01 | 0.07 | 0.00 | 0.01 | 0.02 | 0.44 | 0.01 | 0.00 | 0.03 | 0.03 | 0.07 | 0.03 | 0.05 | 0.02 | 0.04 | 0.03 | 0.02 | 0.05 | 0.03 | 0.05 | 0.05 | 0.01 | 0.03 | 0.03 | 0.06 | 0.01 | 0.02 | 0.06 | 0.01 | 0.00 | 0.18 | 0.08 | 0.01 | 0.00 | 0.06 | 0.00 | 0.00 | 0.11 | 0.03 | 0.17 | 0.22 | 0.04 | 0.01 | 0.21 | 0.03 | 0.61 | 0.11 | 0.24 | 0.01 | 0.04 | 0.05 | 0.00 | 0.00 | 0.00 | 0.05 | 0.03 | 0.01 | 0.01 | 0.02 | 0.00 | 0.00 | 0.02 | 0.05 |
| SLC24A5 | ENSG00000188467 | 0.00 | 0.00 | 0.00 | 0.01 | 0.14 | 0.00 | 0.01 | 0.04 | 0.03 | 0.05 | 0.00 | 0.00 | 0.02 | 0.18 | 0.01 | 0.06 | 0.03 | 0.06 | 0.02 | 0.03 | 0.02 | 0.04 | 0.01 | 0.06 | 0.01 | 0.04 | 0.00 | 0.05 | 0.00 | 0.02 | 0.00 | 0.02 | 0.00 | 0.01 | 0.02 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.08 | 0.06 | 0.25 | 0.00 | 0.10 | 0.00 | 0.07 | 0.08 | 0.26 | 0.06 | 0.07 | 0.01 | 0.03 | 0.00 | 0.00 | 0.02 | 0.05 | 0.00 | 0.03 | 0.00 | 0.11 | 0.00 | 0.00 | 0.03 | 0.13 |
| ITGA2 | ENSG00000164171 | 0.00 | 0.00 | 0.00 | 0.01 | 0.03 | 0.00 | 0.01 | 0.15 | 0.05 | 0.11 | 0.00 | 0.00 | 0.01 | 0.01 | 0.06 | 0.06 | 0.05 | 0.09 | 0.03 | 0.08 | 0.03 | 0.13 | 0.03 | 0.09 | 0.04 | 0.04 | 0.02 | 0.04 | 0.00 | 0.05 | 0.02 | 0.02 | 0.00 | 0.10 | 0.09 | 0.01 | 0.00 | 0.05 | 0.00 | 0.00 | 0.03 | 0.08 | 0.10 | 0.41 | 0.04 | 0.08 | 0.03 | 0.11 | 0.04 | 0.27 | 0.08 | 0.05 | 0.00 | 0.02 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.04 | 0.02 |
| ITGA6 | ENSG00000091409 | 0.02 | 0.00 | 0.07 | 0.00 | 0.00 | 0.00 | 0.01 | 0.08 | 0.06 | 0.04 | 0.00 | 0.01 | 0.00 | 0.00 | 0.05 | 0.01 | 0.14 | 0.02 | 0.16 | 0.01 | 0.26 | 0.01 | 0.05 | 0.04 | 0.01 | 0.01 | 0.03 | 0.02 | 0.06 | 0.02 | 0.06 | 0.05 | 0.05 | 0.01 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.04 | 0.38 | 0.03 | 0.10 | 0.01 | 0.08 | 0.01 | 0.11 | 0.00 | 0.03 | 0.11 | 0.04 | 0.01 | 0.00 | 0.00 | 0.00 | 0.07 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.02 |
| S1PR2 | ENSG00000267534 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.10 | 0.04 | 0.00 | 0.01 | 0.09 | 0.01 | 0.03 | 0.04 | 0.08 | 0.06 | 0.05 | 0.04 | 0.06 | 0.06 | 0.05 | 0.04 | 0.02 | 0.01 | 0.01 | 0.04 | 0.01 | 0.03 | 0.04 | 0.11 | 0.00 | 0.01 | 0.13 | 0.03 | 0.01 | 0.00 | 0.00 | 0.01 | 0.10 | 0.04 | 0.59 | 0.19 | 0.11 | 0.06 | 0.20 | 0.08 | 0.64 | 0.18 | 0.27 | 0.03 | 0.02 | 0.00 | 0.03 | 0.00 | 0.00 | 0.03 | 0.01 | 0.00 | 0.05 | 0.00 | 0.04 | 0.02 | 0.03 | 0.01 |
| SLC52A1 | ENSG00000132517 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.09 | 0.05 | 0.03 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.05 | 0.03 | 0.02 | 0.03 | 0.03 | 0.04 | 0.05 | 0.02 | 0.01 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.12 | 0.00 | 0.05 | 0.02 | 0.05 | 0.00 | 0.03 | 0.00 | 0.00 | 0.03 | 0.05 | 0.10 | 0.05 | 0.01 | 0.03 | 0.03 | 0.03 | 0.15 | 0.15 | 0.16 | 0.27 | 0.00 | 0.02 | 0.00 | 0.02 | 0.00 | 0.06 | 0.00 | 0.00 | 0.00 | 0.06 | 0.00 | 0.00 | 0.05 | 0.03 |
| C16orf89 | ENSG00000153446 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.01 | 0.15 | 0.00 | 0.00 | 0.05 | 0.02 | 0.04 | 0.03 | 0.06 | 0.08 | 0.04 | 0.03 | 0.02 | 0.07 | 0.04 | 0.06 | 0.03 | 0.03 | 0.02 | 0.02 | 0.02 | 0.02 | 0.04 | 0.03 | 0.05 | 0.05 | 0.12 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.08 | 0.02 | 0.14 | 0.15 | 0.11 | 0.01 | 0.04 | 0.02 | 0.06 | 0.12 | 0.10 | 0.06 | 0.00 | 0.00 | 0.00 | 0.00 | 0.09 | 0.00 | 0.01 | 0.00 | 0.02 | 0.01 | 0.00 | 0.00 | 0.06 | 0.01 |
| SLC17A4 | ENSG00000146039 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.01 | 0.27 | 0.02 | 0.00 | 0.01 | 0.02 | 0.03 | 0.07 | 0.02 | 0.07 | 0.06 | 0.02 | 0.05 | 0.10 | 0.11 | 0.04 | 0.04 | 0.04 | 0.03 | 0.04 | 0.03 | 0.03 | 0.03 | 0.11 | 0.01 | 0.06 | 0.08 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.14 | 0.03 | 0.37 | 0.05 | 0.09 | 0.04 | 0.05 | 0.01 | 0.20 | 0.02 | 0.04 | 0.07 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.01 | 0.02 | 0.00 | 0.16 | 0.00 | 0.16 | 0.01 |
| NCSTN | ENSG00000162736 | 0.03 | 0.00 | 0.01 | 0.01 | 0.00 | 0.03 | 0.02 | 0.05 | 0.74 | 0.00 | 0.02 | 0.00 | 0.10 | 0.01 | 0.28 | 0.00 | 0.28 | 0.00 | 0.06 | 0.00 | 0.28 | 0.00 | 0.14 | 0.00 | 0.03 | 0.00 | 0.11 | 0.00 | 0.06 | 0.00 | 0.28 | 0.00 | 0.30 | 0.01 | 0.16 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.28 | 0.01 | 0.41 | 0.02 | 0.16 | 0.00 | 0.15 | 0.00 | 0.28 | 0.00 | 0.45 | 0.02 | 0.11 | 0.00 | 0.00 | 0.00 | 0.24 | 0.00 | 0.02 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.18 | 0.00 |
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