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 |
| LTC4S | ENSG00000213316 | 0.33 | 0.01 | 0.06 | 0.01 | 0.00 | 0.00 | 0.04 | 0.01 | 0.02 | 0.10 | 0.00 | 0.01 | 0.03 | 0.05 | 0.09 | 0.04 | 0.04 | 0.06 | 0.03 | 0.07 | 0.17 | 0.03 | 0.03 | 0.04 | 0.03 | 0.01 | 0.04 | 0.03 | 0.03 | 0.01 | 0.16 | 0.02 | 0.05 | 0.01 | 0.37 | 0.03 | 0.01 | 0.03 | 0.01 | 0.00 | 0.10 | 0.04 | 0.25 | 0.15 | 0.03 | 0.06 | 0.08 | 0.03 | 0.19 | 0.02 | 0.19 | 0.09 | 0.00 | 0.01 | 0.00 | 0.02 | 0.02 | 0.00 | 0.01 | 0.06 | 0.03 | 0.04 | 0.04 | 0.02 | 0.09 | 0.07 |
| CHUK | ENSG00000213341 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.11 | 0.02 | 0.12 | 0.00 | 0.02 | 0.00 | 0.16 | 0.01 | 0.03 | 0.03 | 0.07 | 0.00 | 0.06 | 0.02 | 0.08 | 0.02 | 0.09 | 0.00 | 0.10 | 0.00 | 0.07 | 0.01 | 0.03 | 0.02 | 0.06 | 0.11 | 0.14 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.03 | 0.08 | 0.06 | 0.34 | 0.01 | 0.07 | 0.02 | 0.09 | 0.05 | 0.09 | 0.02 | 0.05 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.07 | 0.01 | 0.04 | 0.00 | 0.05 | 0.00 | 0.00 | 0.01 | 0.04 |
| GSTM2 | ENSG00000213366 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.05 | 0.07 | 0.06 | 0.00 | 0.00 | 0.00 | 0.33 | 0.01 | 0.13 | 0.01 | 0.14 | 0.00 | 0.12 | 0.06 | 0.12 | 0.02 | 0.07 | 0.00 | 0.06 | 0.00 | 0.07 | 0.00 | 0.02 | 0.02 | 0.03 | 0.00 | 0.11 | 0.04 | 0.04 | 0.00 | 0.26 | 0.00 | 0.00 | 0.04 | 0.10 | 0.17 | 0.14 | 0.01 | 0.08 | 0.05 | 0.03 | 0.08 | 0.06 | 0.05 | 0.10 | 0.03 | 0.04 | 0.00 | 0.00 | 0.00 | 0.05 | 0.01 | 0.01 | 0.01 | 0.02 | 0.00 | 0.03 | 0.07 | 0.10 |
| GPC2 | ENSG00000213420 | 0.01 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.04 | 0.01 | 0.08 | 0.01 | 0.00 | 0.00 | 0.03 | 0.00 | 0.12 | 0.01 | 0.22 | 0.02 | 0.22 | 0.00 | 0.52 | 0.02 | 0.30 | 0.01 | 0.02 | 0.01 | 0.01 | 0.00 | 0.10 | 0.01 | 0.07 | 0.02 | 0.14 | 0.01 | 0.10 | 0.03 | 0.00 | 0.02 | 0.00 | 0.00 | 0.08 | 0.03 | 0.22 | 0.05 | 0.08 | 0.01 | 0.10 | 0.01 | 0.28 | 0.03 | 0.07 | 0.04 | 0.06 | 0.01 | 0.00 | 0.00 | 0.13 | 0.00 | 0.06 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.04 | 0.03 |
| S1PR3 | ENSG00000213694 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.01 | 0.05 | 0.04 | 0.00 | 0.02 | 0.01 | 0.05 | 0.01 | 0.04 | 0.04 | 0.03 | 0.03 | 0.00 | 0.07 | 0.01 | 0.02 | 0.04 | 0.02 | 0.01 | 0.04 | 0.01 | 0.00 | 0.00 | 0.01 | 0.02 | 0.03 | 0.15 | 0.02 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.04 | 0.03 | 0.05 | 0.14 | 0.00 | 0.02 | 0.05 | 0.03 | 0.04 | 0.15 | 0.11 | 0.01 | 0.04 | 0.02 | 0.00 | 0.02 | 0.05 | 0.02 | 0.00 | 0.00 | 0.01 | 0.03 | 0.00 | 0.00 | 0.00 | 0.02 |
| SLC35F6 | ENSG00000213699 | 0.00 | 0.00 | 0.02 | 0.01 | 0.00 | 0.00 | 0.01 | 0.01 | 0.09 | 0.01 | 0.00 | 0.00 | 0.03 | 0.08 | 0.06 | 0.02 | 0.09 | 0.01 | 0.03 | 0.01 | 0.07 | 0.04 | 0.04 | 0.03 | 0.01 | 0.00 | 0.02 | 0.02 | 0.01 | 0.04 | 0.09 | 0.00 | 0.00 | 0.05 | 0.01 | 0.03 | 0.01 | 0.00 | 0.00 | 0.00 | 0.06 | 0.03 | 0.20 | 0.09 | 0.08 | 0.00 | 0.10 | 0.02 | 0.22 | 0.00 | 0.04 | 0.09 | 0.17 | 0.01 | 0.00 | 0.00 | 0.02 | 0.02 | 0.00 | 0.00 | 0.01 | 0.02 | 0.05 | 0.00 | 0.01 | 0.04 |
| UGT2B11 | ENSG00000213759 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.04 | 0.12 | 0.03 | 0.00 | 0.00 | 0.00 | 0.06 | 0.05 | 0.03 | 0.23 | 0.01 | 0.08 | 0.02 | 0.13 | 0.01 | 0.04 | 0.02 | 0.01 | 0.01 | 0.03 | 0.01 | 0.00 | 0.01 | 0.03 | 0.06 | 0.00 | 0.03 | 0.03 | 0.00 | 0.02 | 0.02 | 0.00 | 0.00 | 0.09 | 0.02 | 0.27 | 0.08 | 0.04 | 0.04 | 0.04 | 0.01 | 0.06 | 0.05 | 0.07 | 0.06 | 0.09 | 0.01 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.02 | 0.00 | 0.02 | 0.00 | 0.00 | 0.02 | 0.04 |
| KLRK1 | ENSG00000213809 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.03 | 0.01 | 0.13 | 0.06 | 0.05 | 0.01 | 0.00 | 0.00 | 0.05 | 0.03 | 0.09 | 0.12 | 0.01 | 0.10 | 0.02 | 0.05 | 0.02 | 0.05 | 0.08 | 0.01 | 0.04 | 0.04 | 0.04 | 0.01 | 0.06 | 0.01 | 0.05 | 0.14 | 0.05 | 0.03 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.10 | 0.05 | 0.31 | 0.10 | 0.01 | 0.02 | 0.03 | 0.03 | 0.00 | 0.03 | 0.11 | 0.13 | 0.56 | 0.00 | 0.00 | 0.03 | 0.00 | 0.08 | 0.10 | 0.01 | 0.02 | 0.05 | 0.00 | 0.01 | 0.05 | 0.03 |
| SLC23A3 | ENSG00000213901 | 0.01 | 0.06 | 0.04 | 0.04 | 0.00 | 0.03 | 0.01 | 0.02 | 0.01 | 0.27 | 0.00 | 0.01 | 0.00 | 0.10 | 0.02 | 0.03 | 0.04 | 0.19 | 0.00 | 0.18 | 0.03 | 0.13 | 0.06 | 0.04 | 0.02 | 0.01 | 0.02 | 0.02 | 0.05 | 0.03 | 0.03 | 0.04 | 0.00 | 0.01 | 0.03 | 0.02 | 0.00 | 0.00 | 0.00 | 0.01 | 0.04 | 0.06 | 0.18 | 0.16 | 0.03 | 0.34 | 0.05 | 0.05 | 0.08 | 0.05 | 0.08 | 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 | 0.03 |
| LTB4R | ENSG00000213903 | 0.00 | 0.01 | 0.03 | 0.01 | 0.00 | 0.00 | 0.01 | 0.01 | 0.09 | 0.06 | 0.00 | 0.00 | 0.00 | 0.02 | 0.15 | 0.03 | 0.09 | 0.07 | 0.05 | 0.07 | 0.11 | 0.04 | 0.05 | 0.04 | 0.02 | 0.02 | 0.01 | 0.06 | 0.01 | 0.03 | 0.09 | 0.01 | 0.00 | 0.02 | 0.26 | 0.03 | 0.00 | 0.01 | 0.00 | 0.00 | 0.10 | 0.03 | 0.18 | 0.13 | 0.03 | 0.02 | 0.05 | 0.03 | 0.11 | 0.12 | 0.22 | 0.04 | 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 |
| LTB4R2 | ENSG00000213906 | 0.00 | 0.00 | 0.03 | 0.01 | 0.00 | 0.00 | 0.01 | 0.01 | 0.09 | 0.06 | 0.00 | 0.00 | 0.00 | 0.02 | 0.15 | 0.03 | 0.09 | 0.07 | 0.05 | 0.07 | 0.11 | 0.04 | 0.05 | 0.04 | 0.02 | 0.02 | 0.01 | 0.06 | 0.00 | 0.03 | 0.09 | 0.01 | 0.00 | 0.02 | 0.26 | 0.03 | 0.00 | 0.01 | 0.00 | 0.00 | 0.10 | 0.03 | 0.18 | 0.13 | 0.03 | 0.02 | 0.05 | 0.03 | 0.11 | 0.12 | 0.22 | 0.04 | 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 |
| DNASE1 | ENSG00000213918 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.01 | 0.21 | 0.00 | 0.00 | 0.04 | 0.02 | 0.04 | 0.04 | 0.03 | 0.10 | 0.03 | 0.03 | 0.01 | 0.07 | 0.03 | 0.09 | 0.03 | 0.03 | 0.02 | 0.03 | 0.02 | 0.02 | 0.03 | 0.03 | 0.05 | 0.05 | 0.12 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.06 | 0.03 | 0.08 | 0.25 | 0.12 | 0.02 | 0.02 | 0.07 | 0.00 | 0.10 | 0.07 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.00 | 0.01 | 0.00 | 0.02 | 0.02 | 0.00 | 0.00 | 0.07 | 0.02 |
| CCL27 | ENSG00000213927 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.10 | 0.03 | 0.00 | 0.00 | 0.02 | 0.10 | 0.05 | 0.02 | 0.36 | 0.04 | 0.21 | 0.02 | 0.25 | 0.01 | 0.16 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.10 | 0.00 | 0.04 | 0.01 | 0.24 | 0.01 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.08 | 0.02 | 0.10 | 0.06 | 0.01 | 0.01 | 0.03 | 0.02 | 0.00 | 0.05 | 0.11 | 0.05 | 0.03 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.06 | 0.06 | 0.00 | 0.03 | 0.07 | 0.05 |
| IFNA7 | ENSG00000214042 | 0.00 | 0.02 | 0.00 | 0.06 | 0.00 | 0.06 | 0.01 | 0.03 | 0.09 | 0.41 | 0.00 | 0.04 | 0.00 | 0.76 | 0.03 | 0.27 | 0.05 | 0.36 | 0.06 | 0.16 | 0.02 | 0.29 | 0.01 | 0.21 | 0.02 | 0.02 | 0.01 | 0.02 | 0.03 | 0.37 | 0.01 | 0.10 | 0.00 | 0.16 | 0.00 | 0.13 | 0.00 | 0.01 | 0.00 | 0.00 | 0.06 | 0.09 | 0.07 | 0.18 | 0.06 | 0.05 | 0.05 | 0.02 | 0.04 | 0.05 | 0.05 | 0.26 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.09 | 0.00 | 0.24 | 0.01 | 1.02 | 0.00 | 0.00 | 0.01 | 0.32 |
| WEE2 | ENSG00000214102 | 0.02 | 0.01 | 0.06 | 0.00 | 0.05 | 0.02 | 0.03 | 0.03 | 0.04 | 0.04 | 0.00 | 0.01 | 0.04 | 0.05 | 0.09 | 0.02 | 0.08 | 0.06 | 0.02 | 0.15 | 0.05 | 0.20 | 0.03 | 0.09 | 0.03 | 0.00 | 0.03 | 0.01 | 0.03 | 0.05 | 0.04 | 0.05 | 0.00 | 0.06 | 0.06 | 0.06 | 0.00 | 0.02 | 0.00 | 0.00 | 0.09 | 0.04 | 0.50 | 0.05 | 0.03 | 0.08 | 0.04 | 0.05 | 0.05 | 0.14 | 0.15 | 0.11 | 0.02 | 0.04 | 0.00 | 0.05 | 0.02 | 0.09 | 0.11 | 0.00 | 0.05 | 0.01 | 0.00 | 0.00 | 0.22 | 0.02 |
| ANG | ENSG00000214274 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.02 | 0.09 | 0.06 | 0.00 | 0.00 | 0.00 | 0.05 | 0.15 | 0.03 | 0.16 | 0.07 | 0.08 | 0.06 | 0.11 | 0.07 | 0.10 | 0.04 | 0.03 | 0.02 | 0.01 | 0.08 | 0.01 | 0.05 | 0.09 | 0.00 | 0.00 | 0.02 | 0.27 | 0.03 | 0.01 | 0.02 | 0.00 | 0.00 | 0.09 | 0.03 | 0.42 | 0.10 | 0.07 | 0.02 | 0.08 | 0.03 | 0.15 | 0.08 | 0.17 | 0.08 | 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 | 0.03 |
| NPS | ENSG00000214285 | 0.00 | 0.03 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.06 | 0.03 | 0.09 | 0.00 | 0.02 | 0.02 | 0.15 | 0.03 | 0.05 | 0.05 | 0.06 | 0.02 | 0.03 | 0.06 | 0.06 | 0.10 | 0.06 | 0.01 | 0.05 | 0.02 | 0.04 | 0.01 | 0.01 | 0.02 | 0.10 | 0.14 | 0.17 | 0.11 | 0.01 | 0.02 | 0.02 | 0.00 | 0.00 | 0.06 | 0.10 | 0.25 | 0.19 | 0.02 | 0.05 | 0.05 | 0.06 | 0.12 | 0.04 | 0.05 | 0.05 | 0.05 | 0.05 | 0.00 | 0.01 | 0.03 | 0.03 | 0.01 | 0.13 | 0.00 | 0.07 | 0.00 | 0.00 | 0.01 | 0.04 |
| SPINK13 | ENSG00000214510 | 0.30 | 0.00 | 0.03 | 0.01 | 0.02 | 0.00 | 0.02 | 0.02 | 0.02 | 0.05 | 0.00 | 0.00 | 0.02 | 0.05 | 0.05 | 0.05 | 0.01 | 0.03 | 0.01 | 0.05 | 0.03 | 0.03 | 0.03 | 0.05 | 0.01 | 0.03 | 0.03 | 0.01 | 0.02 | 0.02 | 0.09 | 0.03 | 0.09 | 0.01 | 0.22 | 0.04 | 0.00 | 0.05 | 0.01 | 0.00 | 0.03 | 0.02 | 0.14 | 0.10 | 0.02 | 0.01 | 0.02 | 0.03 | 0.09 | 0.02 | 0.07 | 0.04 | 0.00 | 0.00 | 0.00 | 0.10 | 0.04 | 0.00 | 0.00 | 0.05 | 0.01 | 0.03 | 0.00 | 0.03 | 0.03 | 0.14 |
| DEFB113 | ENSG00000214642 | 0.00 | 0.01 | 0.01 | 0.02 | 0.00 | 0.00 | 0.01 | 0.01 | 0.09 | 0.04 | 0.00 | 0.00 | 0.00 | 0.02 | 0.08 | 0.02 | 0.21 | 0.04 | 0.05 | 0.03 | 0.27 | 0.03 | 0.15 | 0.01 | 0.02 | 0.01 | 0.12 | 0.01 | 0.01 | 0.01 | 0.09 | 0.00 | 0.00 | 0.03 | 0.03 | 0.00 | 0.00 | 0.05 | 0.00 | 0.00 | 0.11 | 0.04 | 0.20 | 0.06 | 0.08 | 0.04 | 0.04 | 0.01 | 0.20 | 0.03 | 0.07 | 0.03 | 0.02 | 0.01 | 0.00 | 0.00 | 0.09 | 0.02 | 0.01 | 0.00 | 0.00 | 0.04 | 0.01 | 0.00 | 0.03 | 0.02 |
| CAPN14 | ENSG00000214711 | 0.00 | 0.00 | 0.03 | 0.02 | 0.00 | 0.00 | 0.01 | 0.04 | 0.08 | 0.01 | 0.00 | 0.00 | 0.03 | 0.07 | 0.05 | 0.02 | 0.11 | 0.02 | 0.03 | 0.01 | 0.04 | 0.04 | 0.02 | 0.03 | 0.00 | 0.01 | 0.01 | 0.03 | 0.01 | 0.03 | 0.06 | 0.00 | 0.00 | 0.05 | 0.01 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.06 | 0.02 | 0.22 | 0.06 | 0.09 | 0.00 | 0.07 | 0.01 | 0.16 | 0.00 | 0.08 | 0.05 | 0.14 | 0.01 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.01 | 0.02 | 0.01 | 0.05 | 0.00 | 0.01 | 0.02 |
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