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 |
| BPIFA1 | ENSG00000198183 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.02 | 0.01 | 0.21 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.07 | 0.02 | 0.21 | 0.00 | 0.19 | 0.00 | 0.09 | 0.00 | 0.05 | 0.01 | 0.11 | 0.00 | 0.17 | 0.00 | 0.02 | 0.01 | 0.02 | 0.00 | 0.00 | 0.01 | 0.05 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.06 | 0.02 | 0.20 | 0.02 | 0.19 | 0.00 | 0.08 | 0.01 | 0.38 | 0.00 | 0.09 | 0.02 | 0.03 | 0.00 | 0.00 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 | 0.00 | 0.00 | 0.05 | 0.00 |
| CAPN6 | ENSG00000077274 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.04 | 0.03 | 0.00 | 0.00 | 0.04 | 0.05 | 0.01 | 0.12 | 0.01 | 0.03 | 0.01 | 0.08 | 0.02 | 0.05 | 0.01 | 0.02 | 0.01 | 0.02 | 0.01 | 0.01 | 0.02 | 0.02 | 0.01 | 0.03 | 0.00 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.03 | 0.02 | 0.07 | 0.05 | 0.06 | 0.01 | 0.02 | 0.01 | 0.01 | 0.02 | 0.08 | 0.12 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.02 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 |
| FLT3LG | ENSG00000090554 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.01 | 0.11 | 0.04 | 0.00 | 0.02 | 0.00 | 0.06 | 0.02 | 0.07 | 0.05 | 0.10 | 0.04 | 0.02 | 0.07 | 0.05 | 0.07 | 0.03 | 0.01 | 0.02 | 0.02 | 0.03 | 0.03 | 0.05 | 0.05 | 0.04 | 0.00 | 0.07 | 0.26 | 0.02 | 0.00 | 0.03 | 0.00 | 0.00 | 0.12 | 0.04 | 0.04 | 0.31 | 0.05 | 0.06 | 0.06 | 0.05 | 0.15 | 0.18 | 0.04 | 0.18 | 0.00 | 0.04 | 0.01 | 0.00 | 0.07 | 0.05 | 0.01 | 0.13 | 0.03 | 0.12 | 0.00 | 0.00 | 0.02 | 0.02 |
| DNMT3A | ENSG00000119772 | 0.00 | 0.00 | 0.02 | 0.02 | 0.00 | 0.00 | 0.02 | 0.02 | 0.08 | 0.02 | 0.00 | 0.00 | 0.03 | 0.08 | 0.06 | 0.01 | 0.09 | 0.01 | 0.03 | 0.02 | 0.06 | 0.04 | 0.03 | 0.03 | 0.01 | 0.00 | 0.01 | 0.02 | 0.01 | 0.04 | 0.09 | 0.01 | 0.00 | 0.05 | 0.01 | 0.06 | 0.01 | 0.00 | 0.00 | 0.00 | 0.05 | 0.05 | 0.17 | 0.12 | 0.08 | 0.00 | 0.10 | 0.02 | 0.25 | 0.03 | 0.04 | 0.11 | 0.17 | 0.01 | 0.00 | 0.01 | 0.02 | 0.06 | 0.00 | 0.01 | 0.02 | 0.03 | 0.05 | 0.00 | 0.01 | 0.05 |
| RNGTT | ENSG00000111880 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.36 | 0.03 | 0.07 | 0.00 | 0.00 | 0.01 | 0.04 | 0.02 | 0.06 | 0.07 | 0.03 | 0.03 | 0.03 | 0.05 | 0.07 | 0.02 | 0.08 | 0.01 | 0.03 | 0.01 | 0.02 | 0.00 | 0.03 | 0.01 | 0.06 | 0.00 | 0.13 | 0.15 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.05 | 0.11 | 0.15 | 0.12 | 0.02 | 0.01 | 0.02 | 0.02 | 0.16 | 0.05 | 0.07 | 0.13 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.22 | 0.00 | 0.01 | 0.00 | 0.04 | 0.04 | 0.03 | 0.03 | 0.04 |
| CHI3L1 | ENSG00000133048 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.05 | 0.06 | 0.02 | 0.00 | 0.10 | 0.00 | 0.13 | 0.00 | 0.11 | 0.01 | 0.05 | 0.01 | 0.15 | 0.06 | 0.06 | 0.01 | 0.04 | 0.00 | 0.11 | 0.02 | 0.00 | 0.00 | 0.20 | 0.01 | 0.18 | 0.02 | 0.04 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.26 | 0.00 | 0.32 | 0.07 | 0.06 | 0.00 | 0.10 | 0.01 | 0.17 | 0.00 | 0.10 | 0.13 | 0.05 | 0.00 | 0.01 | 0.00 | 0.26 | 0.02 | 0.04 | 0.01 | 0.14 | 0.00 | 0.09 | 0.00 | 0.18 | 0.01 |
| BRSK1 | ENSG00000160469 | 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 | 0.09 | 0.05 | 0.02 | 0.14 | 0.03 | 0.13 | 0.03 | 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 | 0.26 | 0.13 | 0.06 | 0.06 | 0.05 | 0.36 | 0.10 | 0.04 | 0.19 | 0.00 | 0.06 | 0.01 | 0.00 | 0.26 | 0.03 | 0.02 | 0.19 | 0.03 | 0.12 | 0.00 | 0.00 | 0.03 | 0.05 |
| GPR153 | ENSG00000158292 | 0.00 | 0.06 | 0.01 | 0.09 | 0.00 | 0.00 | 0.01 | 0.05 | 0.10 | 0.09 | 0.00 | 0.02 | 0.04 | 0.31 | 0.07 | 0.05 | 0.08 | 0.11 | 0.06 | 0.09 | 0.20 | 0.09 | 0.10 | 0.10 | 0.02 | 0.14 | 0.00 | 0.20 | 0.04 | 0.06 | 0.02 | 0.32 | 0.00 | 1.09 | 0.03 | 0.21 | 0.01 | 0.11 | 0.00 | 0.00 | 0.03 | 0.19 | 0.26 | 0.35 | 0.06 | 0.10 | 0.07 | 0.12 | 0.13 | 0.27 | 0.17 | 0.25 | 0.09 | 0.12 | 0.02 | 0.01 | 0.04 | 0.15 | 0.00 | 0.07 | 0.02 | 0.28 | 0.00 | 0.05 | 0.06 | 0.15 |
| GALNT2 | ENSG00000143641 | 0.01 | 0.02 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.09 | 0.12 | 0.05 | 0.02 | 0.02 | 0.05 | 0.03 | 0.09 | 0.01 | 0.12 | 0.02 | 0.05 | 0.00 | 0.22 | 0.04 | 0.11 | 0.03 | 0.03 | 0.03 | 0.06 | 0.02 | 0.01 | 0.01 | 0.15 | 0.02 | 0.23 | 0.02 | 0.04 | 0.00 | 0.00 | 0.04 | 0.00 | 0.00 | 0.24 | 0.02 | 0.44 | 0.06 | 0.08 | 0.02 | 0.09 | 0.01 | 0.23 | 0.00 | 0.03 | 0.23 | 0.04 | 0.04 | 0.02 | 0.00 | 0.02 | 0.15 | 0.00 | 0.02 | 0.02 | 0.05 | 0.09 | 0.03 | 0.15 | 0.03 |
| FSTL1 | ENSG00000163430 | 0.00 | 0.01 | 0.01 | 0.00 | 0.02 | 0.00 | 0.02 | 0.02 | 0.06 | 0.02 | 0.00 | 0.01 | 0.00 | 0.01 | 0.04 | 0.02 | 0.13 | 0.02 | 0.04 | 0.00 | 0.07 | 0.06 | 0.05 | 0.01 | 0.00 | 0.00 | 0.03 | 0.01 | 0.00 | 0.00 | 0.02 | 0.01 | 0.00 | 0.02 | 0.03 | 0.01 | 0.00 | 0.05 | 0.00 | 0.00 | 0.03 | 0.04 | 0.25 | 0.02 | 0.06 | 0.01 | 0.05 | 0.01 | 0.07 | 0.08 | 0.10 | 0.07 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.02 | 0.00 | 0.06 | 0.00 | 0.00 | 0.01 | 0.04 |
| KCNN3 | ENSG00000143603 | 0.04 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.07 | 0.01 | 0.37 | 0.01 | 0.02 | 0.00 | 0.11 | 0.00 | 0.38 | 0.00 | 0.26 | 0.00 | 0.06 | 0.00 | 0.21 | 0.01 | 0.18 | 0.00 | 0.03 | 0.00 | 0.11 | 0.00 | 0.09 | 0.00 | 0.38 | 0.00 | 0.53 | 0.01 | 0.21 | 0.00 | 0.10 | 0.00 | 0.00 | 0.00 | 0.34 | 0.00 | 0.52 | 0.02 | 0.20 | 0.00 | 0.17 | 0.00 | 0.56 | 0.00 | 0.40 | 0.01 | 0.09 | 0.00 | 0.00 | 0.00 | 0.25 | 0.02 | 0.02 | 0.00 | 0.05 | 0.00 | 0.00 | 0.00 | 0.23 | 0.01 |
| F8 | ENSG00000185010 | 0.03 | 0.02 | 0.02 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.12 | 0.04 | 0.06 | 0.00 | 0.06 | 0.03 | 0.23 | 0.02 | 0.19 | 0.04 | 0.14 | 0.01 | 0.21 | 0.02 | 0.16 | 0.04 | 0.05 | 0.01 | 0.11 | 0.01 | 0.06 | 0.01 | 0.13 | 0.03 | 0.10 | 0.02 | 0.13 | 0.02 | 0.00 | 0.01 | 0.00 | 0.01 | 0.10 | 0.03 | 0.45 | 0.13 | 0.23 | 0.02 | 0.10 | 0.04 | 0.09 | 0.10 | 0.24 | 0.13 | 0.01 | 0.03 | 0.00 | 0.00 | 0.15 | 0.07 | 0.02 | 0.03 | 0.03 | 0.02 | 0.05 | 0.00 | 0.07 | 0.01 |
| PTPN23 | ENSG00000076201 | 0.00 | 0.18 | 0.00 | 0.02 | 0.05 | 0.00 | 0.00 | 0.04 | 0.03 | 0.13 | 0.00 | 0.04 | 0.00 | 0.57 | 0.00 | 0.06 | 0.01 | 0.09 | 0.00 | 0.05 | 0.04 | 0.10 | 0.01 | 0.11 | 0.00 | 0.05 | 0.02 | 0.06 | 0.01 | 0.05 | 0.04 | 0.06 | 0.00 | 0.24 | 0.03 | 0.02 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.15 | 0.08 | 0.20 | 0.01 | 0.05 | 0.04 | 0.05 | 0.02 | 0.22 | 0.04 | 0.13 | 0.03 | 0.04 | 0.00 | 0.01 | 0.00 | 0.14 | 0.00 | 0.06 | 0.01 | 0.04 | 0.00 | 0.03 | 0.01 | 0.05 |
| SYNJ1 | ENSG00000159082 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.07 | 0.01 | 0.00 | 0.02 | 0.00 | 0.01 | 0.02 | 0.03 | 0.03 | 0.03 | 0.01 | 0.02 | 0.03 | 0.00 | 0.04 | 0.01 | 0.01 | 0.02 | 0.00 | 0.06 | 0.03 | 0.01 | 0.02 | 0.02 | 0.00 | 0.03 | 0.10 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.02 | 0.12 | 0.05 | 0.02 | 0.03 | 0.03 | 0.00 | 0.13 | 0.07 | 0.11 | 0.04 | 0.02 | 0.00 | 0.05 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.02 | 0.02 | 0.04 | 0.00 | 0.01 | 0.01 |
| GAS6 | ENSG00000183087 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.03 | 0.21 | 0.02 | 0.00 | 0.01 | 0.01 | 0.02 | 0.11 | 0.09 | 0.22 | 0.05 | 0.15 | 0.01 | 0.17 | 0.04 | 0.15 | 0.04 | 0.11 | 0.01 | 0.17 | 0.02 | 0.02 | 0.02 | 0.29 | 0.00 | 0.06 | 0.04 | 0.13 | 0.03 | 0.01 | 0.00 | 0.00 | 0.00 | 0.16 | 0.05 | 0.27 | 0.16 | 0.23 | 0.01 | 0.09 | 0.03 | 0.33 | 0.12 | 0.42 | 0.10 | 0.01 | 0.02 | 0.00 | 0.01 | 0.02 | 0.12 | 0.04 | 0.04 | 0.03 | 0.02 | 0.08 | 0.00 | 0.05 | 0.09 |
| SEMA3F | ENSG00000001617 | 0.00 | 0.18 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.02 | 0.03 | 0.16 | 0.02 | 0.00 | 0.00 | 0.57 | 0.01 | 0.06 | 0.00 | 0.11 | 0.00 | 0.06 | 0.03 | 0.14 | 0.02 | 0.11 | 0.00 | 0.06 | 0.01 | 0.06 | 0.00 | 0.05 | 0.07 | 0.05 | 0.00 | 0.20 | 0.01 | 0.02 | 0.01 | 0.02 | 0.00 | 0.00 | 0.01 | 0.17 | 0.09 | 0.18 | 0.01 | 0.06 | 0.10 | 0.07 | 0.10 | 0.27 | 0.03 | 0.16 | 0.02 | 0.03 | 0.00 | 0.01 | 0.00 | 0.06 | 0.02 | 0.05 | 0.02 | 0.04 | 0.00 | 0.03 | 0.01 | 0.04 |
| ADAMTS16 | ENSG00000145536 | 0.00 | 0.00 | 0.02 | 0.02 | 0.03 | 0.06 | 0.04 | 0.02 | 0.19 | 0.03 | 0.00 | 0.01 | 0.06 | 0.00 | 0.33 | 0.01 | 0.31 | 0.01 | 0.11 | 0.03 | 0.18 | 0.03 | 0.09 | 0.02 | 0.02 | 0.02 | 0.02 | 0.02 | 0.03 | 0.01 | 0.07 | 0.02 | 0.00 | 0.05 | 0.15 | 0.10 | 0.00 | 0.00 | 0.00 | 0.00 | 0.09 | 0.02 | 0.36 | 0.04 | 0.14 | 0.02 | 0.11 | 0.01 | 0.08 | 0.03 | 0.21 | 0.07 | 0.01 | 0.02 | 0.00 | 0.00 | 0.06 | 0.00 | 0.00 | 0.06 | 0.01 | 0.04 | 0.00 | 0.02 | 0.17 | 0.08 |
| CD1A | ENSG00000158477 | 0.03 | 0.00 | 0.01 | 0.01 | 0.00 | 0.03 | 0.02 | 0.05 | 0.39 | 0.01 | 0.02 | 0.00 | 0.11 | 0.00 | 0.27 | 0.01 | 0.25 | 0.00 | 0.06 | 0.00 | 0.25 | 0.00 | 0.13 | 0.00 | 0.03 | 0.00 | 0.11 | 0.00 | 0.07 | 0.00 | 0.29 | 0.00 | 0.41 | 0.01 | 0.16 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.27 | 0.01 | 0.38 | 0.02 | 0.15 | 0.00 | 0.15 | 0.00 | 0.29 | 0.00 | 0.38 | 0.03 | 0.11 | 0.00 | 0.00 | 0.00 | 0.25 | 0.00 | 0.01 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.17 | 0.01 |
| NTRK2 | ENSG00000148053 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.04 | 0.03 | 0.00 | 0.02 | 0.01 | 0.07 | 0.00 | 0.03 | 0.03 | 0.03 | 0.01 | 0.01 | 0.07 | 0.01 | 0.02 | 0.03 | 0.01 | 0.01 | 0.02 | 0.01 | 0.00 | 0.00 | 0.01 | 0.02 | 0.00 | 0.15 | 0.02 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.03 | 0.04 | 0.04 | 0.12 | 0.00 | 0.03 | 0.03 | 0.03 | 0.00 | 0.15 | 0.18 | 0.00 | 0.03 | 0.02 | 0.00 | 0.03 | 0.05 | 0.02 | 0.00 | 0.00 | 0.02 | 0.02 | 0.00 | 0.00 | 0.01 | 0.02 |
| IL21R | ENSG00000103522 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.13 | 0.02 | 0.00 | 0.00 | 0.00 | 0.04 | 0.06 | 0.01 | 0.10 | 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 | 0.05 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.02 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.01 |
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