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 |
| KLHL24 | ENSG00000114796 | 0.05 | 0.00 | 0.04 | 0.01 | 0.00 | 0.01 | 0.04 | 0.03 | 0.19 | 0.01 | 0.00 | 0.00 | 0.00 | 0.10 | 0.16 | 0.05 | 2.02 | 0.00 | 0.68 | 0.00 | 0.76 | 0.02 | 0.26 | 0.01 | 0.04 | 0.00 | 0.06 | 0.03 | 0.03 | 0.01 | 0.13 | 0.02 | 0.12 | 0.01 | 0.12 | 0.00 | 0.00 | 0.10 | 0.00 | 0.00 | 0.21 | 0.02 | 1.11 | 0.02 | 0.65 | 0.00 | 0.35 | 0.01 | 0.86 | 0.09 | 0.10 | 0.10 | 0.20 | 0.00 | 0.00 | 0.01 | 0.06 | 0.00 | 0.07 | 0.00 | 0.22 | 0.02 | 0.00 | 0.00 | 0.02 | 0.05 |
| SCMH1 | ENSG00000010803 | 0.00 | 0.02 | 0.01 | 0.03 | 0.00 | 0.00 | 0.00 | 0.01 | 0.26 | 0.03 | 0.00 | 0.00 | 0.11 | 0.03 | 0.13 | 0.02 | 0.11 | 0.03 | 0.09 | 0.02 | 0.28 | 0.02 | 0.08 | 0.03 | 0.04 | 0.02 | 0.04 | 0.01 | 0.08 | 0.00 | 0.03 | 0.10 | 0.00 | 0.26 | 0.03 | 0.03 | 0.03 | 0.08 | 0.00 | 0.00 | 0.09 | 0.04 | 0.72 | 0.05 | 0.08 | 0.01 | 0.15 | 0.01 | 0.28 | 0.05 | 0.12 | 0.04 | 0.05 | 0.03 | 0.02 | 0.00 | 0.00 | 0.05 | 0.00 | 0.01 | 0.04 | 0.02 | 0.00 | 0.10 | 0.04 | 0.03 |
| SLC29A1 | ENSG00000112759 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.20 | 0.02 | 0.00 | 0.00 | 0.01 | 0.02 | 0.12 | 0.01 | 0.14 | 0.05 | 0.06 | 0.02 | 0.58 | 0.02 | 0.37 | 0.01 | 0.10 | 0.00 | 0.20 | 0.00 | 0.03 | 0.00 | 0.15 | 0.00 | 0.05 | 0.01 | 0.08 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.13 | 0.03 | 0.24 | 0.06 | 0.08 | 0.02 | 0.07 | 0.01 | 0.08 | 0.03 | 0.24 | 0.04 | 0.06 | 0.01 | 0.00 | 0.00 | 0.09 | 0.05 | 0.01 | 0.00 | 0.03 | 0.01 | 0.02 | 0.00 | 0.06 | 0.00 |
| IFNGR2 | ENSG00000159128 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.07 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.03 | 0.02 | 0.03 | 0.03 | 0.07 | 0.02 | 0.04 | 0.00 | 0.06 | 0.01 | 0.02 | 0.01 | 0.01 | 0.02 | 0.01 | 0.00 | 0.02 | 0.01 | 0.05 | 0.03 | 0.13 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.06 | 0.01 | 0.11 | 0.04 | 0.02 | 0.01 | 0.03 | 0.00 | 0.07 | 0.03 | 0.04 | 0.04 | 0.02 | 0.00 | 0.05 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.01 | 0.03 | 0.00 | 0.01 | 0.01 |
| SLC6A6 | ENSG00000131389 | 0.00 | 0.18 | 0.00 | 0.01 | 0.07 | 0.00 | 0.00 | 0.01 | 0.36 | 0.02 | 0.00 | 0.03 | 0.03 | 0.03 | 0.03 | 0.05 | 0.01 | 0.05 | 0.03 | 0.02 | 0.05 | 0.03 | 0.06 | 0.05 | 0.01 | 0.03 | 0.03 | 0.06 | 0.01 | 0.02 | 0.06 | 0.01 | 0.00 | 0.18 | 0.07 | 0.01 | 0.00 | 0.04 | 0.00 | 0.00 | 0.14 | 0.03 | 0.14 | 0.22 | 0.03 | 0.01 | 0.07 | 0.04 | 0.05 | 0.11 | 0.25 | 0.02 | 0.05 | 0.05 | 0.00 | 0.00 | 0.00 | 0.05 | 0.03 | 0.01 | 0.02 | 0.02 | 0.00 | 0.00 | 0.03 | 0.05 |
| PDGFC | ENSG00000145431 | 0.00 | 0.03 | 0.00 | 0.03 | 0.06 | 0.02 | 0.02 | 0.04 | 0.06 | 0.13 | 0.00 | 0.00 | 0.02 | 0.03 | 0.04 | 0.06 | 0.02 | 0.12 | 0.01 | 0.10 | 0.12 | 0.11 | 0.07 | 0.08 | 0.01 | 0.07 | 0.02 | 0.04 | 0.00 | 0.03 | 0.06 | 0.06 | 0.00 | 0.12 | 0.10 | 0.05 | 0.00 | 0.03 | 0.00 | 0.00 | 0.05 | 0.08 | 0.08 | 0.28 | 0.02 | 0.08 | 0.02 | 0.05 | 0.12 | 0.05 | 0.11 | 0.13 | 0.01 | 0.02 | 0.00 | 0.00 | 0.03 | 0.03 | 0.00 | 0.09 | 0.00 | 0.03 | 0.00 | 0.00 | 0.05 | 0.06 |
| CARM1 | ENSG00000142453 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.02 | 0.09 | 0.05 | 0.00 | 0.01 | 0.09 | 0.01 | 0.01 | 0.05 | 0.08 | 0.07 | 0.06 | 0.03 | 0.07 | 0.07 | 0.06 | 0.04 | 0.02 | 0.02 | 0.03 | 0.02 | 0.01 | 0.03 | 0.02 | 0.11 | 0.00 | 0.01 | 0.16 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.09 | 0.04 | 0.59 | 0.19 | 0.13 | 0.05 | 0.26 | 0.04 | 0.65 | 0.10 | 0.29 | 0.02 | 0.02 | 0.00 | 0.03 | 0.00 | 0.00 | 0.06 | 0.01 | 0.00 | 0.05 | 0.01 | 0.07 | 0.02 | 0.03 | 0.02 |
| MMRN2 | ENSG00000173269 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.19 | 0.05 | 0.08 | 0.00 | 0.02 | 0.01 | 0.12 | 0.01 | 0.03 | 0.03 | 0.09 | 0.01 | 0.07 | 0.02 | 0.12 | 0.04 | 0.11 | 0.01 | 0.09 | 0.00 | 0.07 | 0.01 | 0.02 | 0.03 | 0.06 | 0.25 | 0.02 | 0.03 | 0.01 | 0.00 | 0.01 | 0.00 | 0.01 | 0.03 | 0.09 | 0.10 | 0.27 | 0.02 | 0.06 | 0.07 | 0.08 | 0.01 | 0.12 | 0.01 | 0.10 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.06 | 0.01 | 0.03 | 0.00 | 0.05 | 0.00 | 0.00 | 0.00 | 0.03 |
| KITLG | ENSG00000049130 | 0.01 | 0.01 | 0.00 | 0.00 | 0.06 | 0.00 | 0.04 | 0.01 | 0.10 | 0.04 | 0.00 | 0.00 | 0.01 | 0.03 | 0.02 | 0.05 | 0.04 | 0.03 | 0.01 | 0.03 | 0.04 | 0.07 | 0.01 | 0.04 | 0.00 | 0.02 | 0.03 | 0.05 | 0.00 | 0.07 | 0.03 | 0.02 | 0.00 | 0.13 | 0.13 | 0.02 | 0.00 | 0.02 | 0.00 | 0.00 | 0.09 | 0.05 | 0.10 | 0.20 | 0.01 | 0.02 | 0.02 | 0.04 | 0.00 | 0.16 | 0.42 | 0.05 | 0.00 | 0.01 | 0.00 | 0.01 | 0.12 | 0.02 | 0.00 | 0.03 | 0.00 | 0.05 | 0.00 | 0.00 | 0.01 | 0.08 |
| TAOK3 | ENSG00000135090 | 0.01 | 0.01 | 0.02 | 0.00 | 0.06 | 0.02 | 0.05 | 0.04 | 0.14 | 0.03 | 0.00 | 0.00 | 0.03 | 0.00 | 0.03 | 0.05 | 0.03 | 0.05 | 0.03 | 0.02 | 0.08 | 0.07 | 0.06 | 0.03 | 0.00 | 0.01 | 0.04 | 0.02 | 0.00 | 0.07 | 0.04 | 0.06 | 0.00 | 0.22 | 0.18 | 0.01 | 0.02 | 0.03 | 0.00 | 0.00 | 0.04 | 0.08 | 0.13 | 0.20 | 0.06 | 0.02 | 0.02 | 0.05 | 0.09 | 0.10 | 0.15 | 0.05 | 0.01 | 0.00 | 0.00 | 0.01 | 0.10 | 0.00 | 0.02 | 0.01 | 0.02 | 0.00 | 0.03 | 0.00 | 0.02 | 0.07 |
| CYP2R1 | ENSG00000186104 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.03 | 0.01 | 0.01 | 0.03 | 0.08 | 0.00 | 0.00 | 0.05 | 0.01 | 0.03 | 0.03 | 0.11 | 0.08 | 0.04 | 0.04 | 0.04 | 0.04 | 0.03 | 0.02 | 0.01 | 0.00 | 0.01 | 0.01 | 0.03 | 0.03 | 0.03 | 0.02 | 0.00 | 0.03 | 0.00 | 0.02 | 0.06 | 0.04 | 0.00 | 0.00 | 0.05 | 0.06 | 0.05 | 0.26 | 0.01 | 0.04 | 0.06 | 0.04 | 0.12 | 0.04 | 0.06 | 0.09 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.04 | 0.01 | 0.02 | 0.00 | 0.00 | 0.03 | 0.01 |
| SLC35B3 | ENSG00000124786 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.06 | 0.25 | 0.05 | 0.00 | 0.05 | 0.03 | 0.02 | 0.10 | 0.01 | 0.09 | 0.08 | 0.05 | 0.06 | 0.09 | 0.22 | 0.04 | 0.10 | 0.02 | 0.03 | 0.02 | 0.04 | 0.03 | 0.07 | 0.15 | 0.02 | 0.06 | 0.06 | 0.06 | 0.06 | 0.00 | 0.01 | 0.00 | 0.00 | 0.15 | 0.05 | 0.46 | 0.09 | 0.08 | 0.06 | 0.08 | 0.02 | 0.19 | 0.05 | 0.05 | 0.14 | 0.04 | 0.03 | 0.00 | 0.00 | 0.10 | 0.01 | 0.02 | 0.02 | 0.01 | 0.03 | 0.27 | 0.00 | 0.26 | 0.01 |
| FRK | ENSG00000111816 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.26 | 0.02 | 0.11 | 0.00 | 0.01 | 0.00 | 0.15 | 0.01 | 0.05 | 0.03 | 0.04 | 0.05 | 0.02 | 0.06 | 0.08 | 0.03 | 0.07 | 0.01 | 0.04 | 0.02 | 0.05 | 0.00 | 0.03 | 0.01 | 0.08 | 0.00 | 0.17 | 0.11 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.10 | 0.08 | 0.07 | 0.27 | 0.01 | 0.02 | 0.05 | 0.02 | 0.07 | 0.05 | 0.28 | 0.05 | 0.00 | 0.03 | 0.00 | 0.00 | 0.01 | 0.18 | 0.00 | 0.04 | 0.00 | 0.08 | 0.06 | 0.03 | 0.01 | 0.14 |
| BTD | ENSG00000169814 | 0.00 | 0.18 | 0.00 | 0.01 | 0.07 | 0.00 | 0.01 | 0.02 | 0.27 | 0.02 | 0.00 | 0.03 | 0.01 | 0.05 | 0.02 | 0.04 | 0.01 | 0.04 | 0.01 | 0.02 | 0.05 | 0.03 | 0.05 | 0.05 | 0.01 | 0.03 | 0.03 | 0.06 | 0.01 | 0.02 | 0.05 | 0.02 | 0.00 | 0.18 | 0.07 | 0.01 | 0.00 | 0.04 | 0.00 | 0.00 | 0.13 | 0.03 | 0.14 | 0.20 | 0.01 | 0.02 | 0.04 | 0.05 | 0.05 | 0.11 | 0.20 | 0.02 | 0.05 | 0.05 | 0.00 | 0.00 | 0.00 | 0.05 | 0.03 | 0.01 | 0.01 | 0.02 | 0.00 | 0.00 | 0.03 | 0.06 |
| SERPING1 | ENSG00000149131 | 0.00 | 0.00 | 0.00 | 0.01 | 0.09 | 0.00 | 0.00 | 0.02 | 0.15 | 0.02 | 0.00 | 0.00 | 0.06 | 0.03 | 0.05 | 0.03 | 0.08 | 0.01 | 0.10 | 0.02 | 0.13 | 0.04 | 0.02 | 0.05 | 0.01 | 0.01 | 0.01 | 0.04 | 0.00 | 0.02 | 0.02 | 0.02 | 0.00 | 0.12 | 0.04 | 0.00 | 0.02 | 0.03 | 0.00 | 0.00 | 0.11 | 0.06 | 0.11 | 0.05 | 0.07 | 0.02 | 0.06 | 0.02 | 0.34 | 0.11 | 0.06 | 0.04 | 0.01 | 0.03 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.02 | 0.01 | 0.03 | 0.00 | 0.00 | 0.04 | 0.02 |
| HIAT1 | ENSG00000156875 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.07 | 0.03 | 0.06 | 0.00 | 0.00 | 0.00 | 0.39 | 0.02 | 0.12 | 0.03 | 0.09 | 0.01 | 0.08 | 0.02 | 0.10 | 0.02 | 0.07 | 0.00 | 0.07 | 0.01 | 0.06 | 0.00 | 0.02 | 0.03 | 0.04 | 0.00 | 0.11 | 0.04 | 0.04 | 0.00 | 0.25 | 0.00 | 0.00 | 0.03 | 0.11 | 0.15 | 0.17 | 0.00 | 0.07 | 0.03 | 0.02 | 0.02 | 0.06 | 0.06 | 0.09 | 0.03 | 0.05 | 0.01 | 0.00 | 0.00 | 0.07 | 0.01 | 0.01 | 0.01 | 0.03 | 0.00 | 0.03 | 0.04 | 0.11 |
| MAP2K7 | ENSG00000076984 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.02 | 0.01 | 0.02 | 0.06 | 0.08 | 0.00 | 0.01 | 0.01 | 0.07 | 0.01 | 0.05 | 0.05 | 0.09 | 0.02 | 0.08 | 0.01 | 0.12 | 0.02 | 0.08 | 0.01 | 0.03 | 0.00 | 0.06 | 0.00 | 0.04 | 0.00 | 0.11 | 0.00 | 0.01 | 0.07 | 0.03 | 0.01 | 0.00 | 0.00 | 0.01 | 0.06 | 0.07 | 0.27 | 0.42 | 0.06 | 0.12 | 0.05 | 0.19 | 0.14 | 0.56 | 0.25 | 0.01 | 0.02 | 0.00 | 0.04 | 0.00 | 0.00 | 0.09 | 0.00 | 0.01 | 0.03 | 0.00 | 0.00 | 0.05 | 0.03 | 0.03 |
| CDC42BPB | ENSG00000198752 | 0.00 | 0.02 | 0.01 | 0.01 | 0.00 | 0.04 | 0.02 | 0.03 | 0.06 | 0.07 | 0.00 | 0.00 | 0.00 | 0.12 | 0.06 | 0.06 | 0.17 | 0.05 | 0.06 | 0.06 | 0.11 | 0.07 | 0.06 | 0.08 | 0.00 | 0.03 | 0.03 | 0.03 | 0.02 | 0.03 | 0.03 | 0.11 | 0.04 | 0.31 | 0.16 | 0.00 | 0.01 | 0.04 | 0.00 | 0.00 | 0.09 | 0.08 | 0.29 | 0.17 | 0.06 | 0.10 | 0.09 | 0.02 | 0.16 | 0.02 | 0.20 | 0.06 | 0.03 | 0.01 | 0.00 | 0.00 | 0.03 | 0.03 | 0.01 | 0.08 | 0.02 | 0.05 | 0.03 | 0.01 | 0.02 | 0.06 |
| MMP15 | ENSG00000102996 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.04 | 0.01 | 0.04 | 0.00 | 0.00 | 0.00 | 0.01 | 0.04 | 0.03 | 0.04 | 0.01 | 0.03 | 0.02 | 0.10 | 0.01 | 0.02 | 0.02 | 0.02 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.02 | 0.02 | 0.00 | 0.01 | 0.06 | 0.06 | 0.00 | 0.02 | 0.00 | 0.00 | 0.02 | 0.04 | 0.04 | 0.14 | 0.00 | 0.06 | 0.03 | 0.07 | 0.02 | 0.16 | 0.02 | 0.05 | 0.12 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.01 | 0.01 | 0.02 | 0.00 | 0.03 | 0.02 | 0.04 |
| RIPK1 | ENSG00000137275 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.04 | 0.19 | 0.11 | 0.00 | 0.06 | 0.02 | 0.01 | 0.10 | 0.02 | 0.09 | 0.10 | 0.05 | 0.06 | 0.09 | 0.24 | 0.05 | 0.10 | 0.02 | 0.03 | 0.02 | 0.06 | 0.00 | 0.09 | 0.18 | 0.02 | 0.06 | 0.08 | 0.08 | 0.05 | 0.01 | 0.01 | 0.00 | 0.00 | 0.09 | 0.08 | 0.44 | 0.11 | 0.10 | 0.06 | 0.09 | 0.02 | 0.24 | 0.05 | 0.06 | 0.14 | 0.04 | 0.03 | 0.00 | 0.00 | 0.10 | 0.01 | 0.02 | 0.04 | 0.03 | 0.03 | 0.22 | 0.00 | 0.23 | 0.00 |
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