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 |
| TIMP2 | ENSG00000035862 | 0.02 | 0.00 | 0.05 | 0.00 | 0.02 | 0.00 | 0.03 | 0.03 | 0.19 | 0.00 | 0.00 | 0.00 | 0.09 | 0.02 | 0.16 | 0.01 | 0.20 | 0.03 | 0.08 | 0.03 | 0.18 | 0.08 | 0.09 | 0.04 | 0.06 | 0.00 | 0.04 | 0.03 | 0.08 | 0.09 | 0.26 | 0.02 | 0.08 | 0.01 | 0.08 | 0.02 | 0.02 | 0.01 | 0.00 | 0.00 | 0.35 | 0.03 | 0.40 | 0.03 | 0.11 | 0.07 | 0.13 | 0.01 | 0.60 | 0.04 | 0.21 | 0.03 | 0.05 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.06 | 0.00 | 0.05 | 0.01 | 0.14 | 0.00 | 0.25 | 0.01 |
| FLT4 | ENSG00000037280 | 0.33 | 0.01 | 0.06 | 0.01 | 0.00 | 0.04 | 0.03 | 0.01 | 0.02 | 0.10 | 0.00 | 0.01 | 0.03 | 0.05 | 0.09 | 0.03 | 0.04 | 0.06 | 0.04 | 0.06 | 0.16 | 0.02 | 0.03 | 0.04 | 0.03 | 0.01 | 0.04 | 0.03 | 0.03 | 0.01 | 0.14 | 0.05 | 0.05 | 0.01 | 0.38 | 0.03 | 0.01 | 0.03 | 0.01 | 0.00 | 0.10 | 0.05 | 0.24 | 0.14 | 0.04 | 0.04 | 0.08 | 0.03 | 0.21 | 0.02 | 0.20 | 0.11 | 0.00 | 0.01 | 0.00 | 0.02 | 0.02 | 0.00 | 0.01 | 0.06 | 0.04 | 0.05 | 0.04 | 0.02 | 0.09 | 0.08 |
| CD36 | ENSG00000135218 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.02 | 0.04 | 0.02 | 0.00 | 0.00 | 0.03 | 0.00 | 0.04 | 0.02 | 0.12 | 0.02 | 0.09 | 0.02 | 0.20 | 0.03 | 0.09 | 0.01 | 0.01 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.05 | 0.01 | 0.04 | 0.01 | 0.03 | 0.01 | 0.00 | 0.02 | 0.00 | 0.00 | 0.07 | 0.03 | 0.13 | 0.08 | 0.04 | 0.01 | 0.02 | 0.02 | 0.12 | 0.03 | 0.09 | 0.05 | 0.07 | 0.00 | 0.00 | 0.00 | 0.10 | 0.00 | 0.01 | 0.00 | 0.07 | 0.01 | 0.00 | 0.03 | 0.04 | 0.02 |
| ADGRL3 | ENSG00000150471 | 0.01 | 0.01 | 0.00 | 0.01 | 0.00 | 0.03 | 0.01 | 0.06 | 0.10 | 0.04 | 0.00 | 0.00 | 0.00 | 0.05 | 0.08 | 0.03 | 0.22 | 0.03 | 0.05 | 0.03 | 0.13 | 0.06 | 0.03 | 0.03 | 0.01 | 0.01 | 0.03 | 0.04 | 0.00 | 0.01 | 0.05 | 0.07 | 0.00 | 0.09 | 0.03 | 0.11 | 0.02 | 0.02 | 0.00 | 0.00 | 0.07 | 0.02 | 0.18 | 0.10 | 0.04 | 0.04 | 0.04 | 0.03 | 0.04 | 0.02 | 0.16 | 0.05 | 0.19 | 0.01 | 0.00 | 0.01 | 0.00 | 0.04 | 0.03 | 0.01 | 0.04 | 0.03 | 0.03 | 0.00 | 0.06 | 0.02 |
| ACTN1 | ENSG00000072110 | 0.01 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.05 | 0.02 | 0.08 | 0.00 | 0.01 | 0.02 | 0.05 | 0.04 | 0.04 | 0.03 | 0.06 | 0.04 | 0.01 | 0.08 | 0.03 | 0.04 | 0.05 | 0.00 | 0.03 | 0.01 | 0.03 | 0.01 | 0.01 | 0.02 | 0.09 | 0.00 | 0.33 | 0.04 | 0.05 | 0.02 | 0.03 | 0.00 | 0.00 | 0.02 | 0.11 | 0.09 | 0.25 | 0.03 | 0.02 | 0.05 | 0.02 | 0.11 | 0.04 | 0.05 | 0.14 | 0.02 | 0.01 | 0.00 | 0.00 | 0.04 | 0.00 | 0.00 | 0.11 | 0.02 | 0.08 | 0.03 | 0.00 | 0.01 | 0.05 |
| ITGAX | ENSG00000140678 | 0.00 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.09 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.10 | 0.01 | 0.09 | 0.01 | 0.02 | 0.02 | 0.06 | 0.00 | 0.06 | 0.01 | 0.04 | 0.00 | 0.06 | 0.00 | 0.00 | 0.00 | 0.04 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.09 | 0.01 | 0.09 | 0.03 | 0.01 | 0.03 | 0.10 | 0.00 | 0.52 | 0.05 | 0.04 | 0.02 | 0.02 | 0.01 | 0.00 | 0.02 | 0.13 | 0.00 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.01 |
| MDK | ENSG00000110492 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.00 | 0.00 | 0.09 | 0.03 | 0.05 | 0.00 | 0.00 | 0.00 | 0.01 | 0.04 | 0.02 | 0.14 | 0.03 | 0.11 | 0.01 | 0.16 | 0.03 | 0.15 | 0.01 | 0.00 | 0.00 | 0.02 | 0.00 | 0.03 | 0.01 | 0.01 | 0.00 | 0.00 | 0.07 | 0.05 | 0.01 | 0.01 | 0.03 | 0.00 | 0.00 | 0.07 | 0.02 | 0.13 | 0.06 | 0.08 | 0.02 | 0.11 | 0.01 | 0.03 | 0.03 | 0.10 | 0.07 | 0.00 | 0.04 | 0.01 | 0.00 | 0.00 | 0.05 | 0.00 | 0.03 | 0.02 | 0.07 | 0.00 | 0.02 | 0.01 | 0.05 |
| TBCK | ENSG00000145348 | 0.00 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.03 | 0.04 | 0.06 | 0.00 | 0.01 | 0.00 | 0.08 | 0.02 | 0.03 | 0.03 | 0.05 | 0.01 | 0.03 | 0.02 | 0.07 | 0.02 | 0.04 | 0.01 | 0.02 | 0.00 | 0.05 | 0.00 | 0.01 | 0.01 | 0.13 | 0.00 | 0.11 | 0.04 | 0.04 | 0.04 | 0.01 | 0.00 | 0.00 | 0.04 | 0.06 | 0.03 | 0.29 | 0.01 | 0.02 | 0.01 | 0.04 | 0.00 | 0.11 | 0.04 | 0.07 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.02 | 0.01 | 0.03 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.05 |
| COL5A3 | ENSG00000080573 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.01 | 0.08 | 0.04 | 0.00 | 0.01 | 0.14 | 0.01 | 0.03 | 0.04 | 0.07 | 0.06 | 0.05 | 0.05 | 0.04 | 0.06 | 0.03 | 0.05 | 0.01 | 0.01 | 0.01 | 0.04 | 0.01 | 0.02 | 0.01 | 0.11 | 0.00 | 0.01 | 0.15 | 0.03 | 0.01 | 0.00 | 0.00 | 0.01 | 0.09 | 0.04 | 0.52 | 0.21 | 0.11 | 0.06 | 0.17 | 0.11 | 0.64 | 0.23 | 0.34 | 0.02 | 0.02 | 0.00 | 0.03 | 0.00 | 0.00 | 0.03 | 0.01 | 0.00 | 0.06 | 0.01 | 0.00 | 0.02 | 0.02 | 0.01 |
| ABCB1 | ENSG00000085563 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.01 | 0.05 | 0.02 | 0.00 | 0.00 | 0.03 | 0.06 | 0.04 | 0.02 | 0.21 | 0.02 | 0.19 | 0.01 | 0.48 | 0.01 | 0.24 | 0.01 | 0.03 | 0.01 | 0.01 | 0.00 | 0.08 | 0.01 | 0.08 | 0.03 | 0.04 | 0.01 | 0.11 | 0.02 | 0.00 | 0.02 | 0.00 | 0.00 | 0.06 | 0.02 | 0.19 | 0.05 | 0.08 | 0.02 | 0.02 | 0.02 | 0.09 | 0.08 | 0.07 | 0.05 | 0.13 | 0.00 | 0.00 | 0.00 | 0.13 | 0.00 | 0.02 | 0.00 | 0.06 | 0.01 | 0.00 | 0.00 | 0.02 | 0.02 |
| OCLN | ENSG00000197822 | 0.00 | 0.01 | 0.00 | 0.01 | 0.03 | 0.01 | 0.00 | 0.23 | 0.01 | 0.16 | 0.00 | 0.01 | 0.00 | 0.05 | 0.01 | 0.08 | 0.01 | 0.10 | 0.01 | 0.08 | 0.01 | 0.16 | 0.02 | 0.14 | 0.00 | 0.07 | 0.00 | 0.06 | 0.00 | 0.07 | 0.01 | 0.04 | 0.00 | 0.13 | 0.05 | 0.00 | 0.00 | 0.04 | 0.00 | 0.00 | 0.01 | 0.10 | 0.01 | 0.74 | 0.00 | 0.06 | 0.01 | 0.11 | 0.06 | 0.35 | 0.03 | 0.05 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.03 | 0.00 | 0.00 | 0.05 | 0.04 |
| WNT5B | ENSG00000111186 | 0.02 | 0.00 | 0.00 | 0.01 | 0.04 | 0.00 | 0.01 | 0.06 | 0.11 | 0.04 | 0.01 | 0.00 | 0.04 | 0.01 | 0.10 | 0.07 | 0.21 | 0.03 | 0.14 | 0.03 | 0.18 | 0.08 | 0.09 | 0.06 | 0.13 | 0.01 | 0.17 | 0.04 | 0.13 | 0.04 | 0.04 | 0.04 | 0.30 | 0.05 | 0.02 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.17 | 0.05 | 0.45 | 0.09 | 0.08 | 0.03 | 0.10 | 0.02 | 0.23 | 0.10 | 0.12 | 0.13 | 0.59 | 0.00 | 0.00 | 0.01 | 0.02 | 0.03 | 0.12 | 0.02 | 0.07 | 0.02 | 0.00 | 0.01 | 0.06 | 0.03 |
| AQP4 | ENSG00000171885 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.03 | 0.00 | 0.02 | 0.06 | 0.04 | 0.00 | 0.00 | 0.03 | 0.03 | 0.13 | 0.02 | 0.22 | 0.04 | 0.16 | 0.05 | 0.18 | 0.07 | 0.10 | 0.06 | 0.01 | 0.03 | 0.02 | 0.04 | 0.05 | 0.05 | 0.00 | 0.01 | 0.00 | 0.08 | 0.05 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.09 | 0.02 | 0.31 | 0.05 | 0.06 | 0.02 | 0.09 | 0.01 | 0.05 | 0.00 | 0.07 | 0.05 | 0.00 | 0.04 | 0.00 | 0.01 | 0.03 | 0.00 | 0.02 | 0.01 | 0.02 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 |
| ITGA8 | ENSG00000077943 | 0.02 | 0.01 | 0.03 | 0.00 | 0.00 | 0.00 | 0.01 | 0.03 | 0.15 | 0.03 | 0.00 | 0.00 | 0.03 | 0.08 | 0.03 | 0.04 | 0.03 | 0.07 | 0.01 | 0.03 | 0.06 | 0.03 | 0.06 | 0.04 | 0.00 | 0.02 | 0.00 | 0.00 | 0.04 | 0.00 | 0.00 | 0.01 | 0.00 | 0.05 | 0.06 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.12 | 0.01 | 0.19 | 0.06 | 0.03 | 0.01 | 0.04 | 0.02 | 0.30 | 0.00 | 0.05 | 0.07 | 0.02 | 0.01 | 0.00 | 0.00 | 0.04 | 0.00 | 0.03 | 0.01 | 0.02 | 0.01 | 0.00 | 0.02 | 0.02 | 0.02 |
| CD247 | ENSG00000198821 | 0.03 | 0.00 | 0.01 | 0.01 | 0.00 | 0.03 | 0.01 | 0.06 | 0.49 | 0.01 | 0.02 | 0.02 | 0.10 | 0.03 | 0.16 | 0.01 | 0.25 | 0.01 | 0.05 | 0.01 | 0.22 | 0.00 | 0.11 | 0.00 | 0.03 | 0.00 | 0.08 | 0.00 | 0.06 | 0.00 | 0.26 | 0.00 | 0.30 | 0.01 | 0.02 | 0.04 | 0.04 | 0.00 | 0.00 | 0.00 | 0.22 | 0.01 | 0.33 | 0.02 | 0.15 | 0.00 | 0.12 | 0.01 | 0.27 | 0.00 | 0.41 | 0.03 | 0.09 | 0.01 | 0.00 | 0.00 | 0.28 | 0.00 | 0.01 | 0.00 | 0.02 | 0.01 | 0.00 | 0.00 | 0.15 | 0.01 |
| PROS1 | ENSG00000184500 | 0.01 | 0.02 | 0.01 | 0.01 | 0.00 | 0.02 | 0.01 | 0.03 | 0.07 | 0.07 | 0.00 | 0.00 | 0.01 | 0.03 | 0.06 | 0.07 | 0.28 | 0.14 | 0.12 | 0.08 | 0.15 | 0.22 | 0.05 | 0.06 | 0.00 | 0.01 | 0.01 | 0.02 | 0.00 | 0.02 | 0.00 | 0.03 | 0.00 | 0.18 | 0.11 | 0.03 | 0.00 | 0.07 | 0.00 | 0.00 | 0.05 | 0.06 | 0.20 | 0.06 | 0.06 | 0.11 | 0.05 | 0.04 | 0.24 | 0.24 | 0.12 | 0.09 | 0.04 | 0.01 | 0.00 | 0.00 | 0.02 | 0.00 | 0.01 | 0.03 | 0.00 | 0.05 | 0.00 | 0.00 | 0.04 | 0.02 |
| ESRRG | ENSG00000196482 | 0.01 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.07 | 0.10 | 0.06 | 0.02 | 0.02 | 0.07 | 0.03 | 0.08 | 0.01 | 0.10 | 0.01 | 0.05 | 0.01 | 0.18 | 0.04 | 0.06 | 0.02 | 0.03 | 0.01 | 0.06 | 0.04 | 0.00 | 0.01 | 0.13 | 0.02 | 0.21 | 0.02 | 0.04 | 0.02 | 0.01 | 0.02 | 0.00 | 0.00 | 0.21 | 0.02 | 0.21 | 0.16 | 0.06 | 0.01 | 0.06 | 0.03 | 0.16 | 0.04 | 0.01 | 0.22 | 0.02 | 0.03 | 0.01 | 0.00 | 0.10 | 0.04 | 0.00 | 0.02 | 0.02 | 0.06 | 0.09 | 0.00 | 0.12 | 0.04 |
| FZD4 | ENSG00000174804 | 0.01 | 0.01 | 0.00 | 0.03 | 0.00 | 0.03 | 0.03 | 0.01 | 0.12 | 0.04 | 0.00 | 0.00 | 0.09 | 0.05 | 0.12 | 0.02 | 0.09 | 0.05 | 0.11 | 0.07 | 0.20 | 0.04 | 0.10 | 0.02 | 0.02 | 0.01 | 0.02 | 0.01 | 0.00 | 0.01 | 0.03 | 0.04 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.00 | 0.16 | 0.08 | 0.49 | 0.06 | 0.16 | 0.07 | 0.07 | 0.03 | 0.06 | 0.19 | 0.07 | 0.09 | 0.04 | 0.06 | 0.00 | 0.00 | 0.00 | 0.05 | 0.01 | 0.01 | 0.02 | 0.01 | 0.00 | 0.00 | 0.10 | 0.07 |
| IL4R | ENSG00000077238 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.13 | 0.03 | 0.00 | 0.00 | 0.00 | 0.04 | 0.06 | 0.01 | 0.09 | 0.01 | 0.03 | 0.01 | 0.05 | 0.00 | 0.05 | 0.00 | 0.04 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.05 | 0.00 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.05 | 0.01 | 0.06 | 0.03 | 0.02 | 0.01 | 0.06 | 0.00 | 0.28 | 0.03 | 0.04 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.02 | 0.00 | 0.03 | 0.00 | 0.00 | 0.01 | 0.02 |
| ATP13A4 | ENSG00000127249 | 0.05 | 0.00 | 0.03 | 0.01 | 0.00 | 0.01 | 0.04 | 0.06 | 0.17 | 0.01 | 0.00 | 0.00 | 0.00 | 0.09 | 0.14 | 0.06 | 1.38 | 0.01 | 0.57 | 0.00 | 0.75 | 0.02 | 0.27 | 0.02 | 0.05 | 0.01 | 0.06 | 0.03 | 0.03 | 0.01 | 0.11 | 0.03 | 0.12 | 0.03 | 0.10 | 0.00 | 0.00 | 0.10 | 0.00 | 0.00 | 0.21 | 0.02 | 1.00 | 0.08 | 0.64 | 0.00 | 0.35 | 0.01 | 0.77 | 0.15 | 0.11 | 0.11 | 0.19 | 0.02 | 0.00 | 0.00 | 0.07 | 0.03 | 0.02 | 0.06 | 0.07 | 0.09 | 0.00 | 0.00 | 0.03 | 0.03 |
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