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 |
| GABBR2 | ENSG00000136928 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.02 | 0.07 | 0.02 | 0.01 | 0.02 | 0.06 | 0.01 | 0.04 | 0.05 | 0.01 | 0.04 | 0.00 | 0.09 | 0.01 | 0.03 | 0.04 | 0.01 | 0.01 | 0.04 | 0.03 | 0.00 | 0.02 | 0.02 | 0.06 | 0.00 | 0.08 | 0.08 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.04 | 0.04 | 0.05 | 0.14 | 0.02 | 0.02 | 0.01 | 0.04 | 0.00 | 0.15 | 0.10 | 0.03 | 0.04 | 0.02 | 0.00 | 0.02 | 0.00 | 0.03 | 0.00 | 0.01 | 0.03 | 0.01 | 0.00 | 0.00 | 0.02 | 0.02 |
| AKT2 | ENSG00000105221 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.02 | 0.01 | 0.03 | 0.23 | 0.02 | 0.00 | 0.00 | 0.08 | 0.02 | 0.17 | 0.03 | 0.47 | 0.05 | 0.07 | 0.02 | 0.05 | 0.05 | 0.07 | 0.02 | 0.07 | 0.01 | 0.01 | 0.01 | 0.25 | 0.01 | 0.08 | 0.02 | 0.12 | 0.01 | 0.15 | 0.04 | 0.00 | 0.02 | 0.00 | 0.00 | 0.13 | 0.03 | 0.53 | 0.20 | 0.20 | 0.04 | 0.19 | 0.03 | 0.93 | 0.11 | 0.25 | 0.11 | 0.00 | 0.03 | 0.01 | 0.00 | 0.05 | 0.00 | 0.02 | 0.06 | 0.03 | 0.05 | 0.00 | 0.00 | 0.03 | 0.01 |
| GPR160 | ENSG00000173890 | 0.07 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.11 | 0.01 | 0.20 | 0.01 | 0.00 | 0.00 | 0.00 | 0.03 | 0.23 | 0.01 | 1.72 | 0.00 | 0.60 | 0.00 | 0.90 | 0.00 | 0.32 | 0.00 | 0.03 | 0.01 | 0.04 | 0.01 | 0.09 | 0.00 | 0.15 | 0.01 | 0.12 | 0.03 | 0.10 | 0.00 | 0.00 | 0.07 | 0.00 | 0.00 | 0.25 | 0.01 | 1.52 | 0.02 | 0.75 | 0.00 | 0.45 | 0.00 | 1.24 | 0.00 | 0.10 | 0.07 | 0.20 | 0.00 | 0.00 | 0.00 | 0.06 | 0.00 | 0.04 | 0.01 | 0.05 | 0.02 | 0.00 | 0.00 | 0.03 | 0.02 |
| ACLY | ENSG00000131473 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.07 | 0.06 | 0.02 | 0.00 | 0.00 | 0.01 | 0.02 | 0.05 | 0.01 | 0.04 | 0.05 | 0.02 | 0.01 | 0.56 | 0.03 | 0.34 | 0.03 | 0.06 | 0.00 | 0.03 | 0.02 | 0.03 | 0.03 | 0.02 | 0.03 | 0.02 | 0.01 | 0.04 | 0.16 | 0.00 | 0.12 | 0.00 | 0.00 | 0.09 | 0.10 | 0.03 | 0.15 | 0.06 | 0.04 | 0.04 | 0.07 | 0.19 | 0.14 | 0.05 | 0.12 | 0.01 | 0.01 | 0.00 | 0.02 | 0.04 | 0.00 | 0.00 | 0.01 | 0.01 | 0.03 | 0.00 | 0.05 | 0.01 | 0.03 |
| C1QL1 | ENSG00000131094 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.12 | 0.03 | 0.02 | 0.01 | 0.00 | 0.03 | 0.00 | 0.05 | 0.01 | 0.05 | 0.04 | 0.01 | 0.01 | 0.14 | 0.02 | 0.07 | 0.02 | 0.02 | 0.00 | 0.03 | 0.04 | 0.05 | 0.01 | 0.04 | 0.02 | 0.02 | 0.01 | 0.01 | 0.08 | 0.00 | 0.07 | 0.00 | 0.00 | 0.03 | 0.10 | 0.02 | 0.11 | 0.02 | 0.02 | 0.03 | 0.07 | 0.00 | 0.18 | 0.04 | 0.07 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.01 | 0.00 | 0.05 | 0.01 | 0.05 |
| SLC7A6 | ENSG00000103064 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.06 | 0.00 | 0.08 | 0.16 | 0.02 | 0.00 | 0.00 | 0.01 | 0.07 | 0.04 | 0.03 | 0.06 | 0.02 | 0.03 | 0.02 | 0.19 | 0.02 | 0.04 | 0.04 | 0.00 | 0.00 | 0.01 | 0.01 | 0.01 | 0.00 | 0.03 | 0.04 | 0.05 | 0.01 | 0.24 | 0.03 | 0.01 | 0.02 | 0.00 | 0.01 | 0.04 | 0.05 | 0.03 | 0.32 | 0.03 | 0.02 | 0.01 | 0.09 | 0.06 | 0.14 | 0.02 | 0.05 | 0.15 | 0.02 | 0.00 | 0.05 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.03 | 0.05 | 0.01 |
| PIK3CB | ENSG00000051382 | 0.03 | 0.01 | 0.05 | 0.00 | 0.00 | 0.00 | 0.07 | 0.02 | 0.07 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.07 | 0.01 | 0.37 | 0.01 | 0.23 | 0.00 | 0.29 | 0.02 | 0.14 | 0.02 | 0.02 | 0.00 | 0.09 | 0.01 | 0.01 | 0.00 | 0.05 | 0.00 | 0.04 | 0.03 | 0.08 | 0.02 | 0.00 | 0.05 | 0.00 | 0.00 | 0.10 | 0.02 | 0.52 | 0.03 | 0.27 | 0.00 | 0.11 | 0.00 | 0.20 | 0.02 | 0.11 | 0.07 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.02 | 0.00 | 0.01 | 0.03 | 0.03 | 0.00 | 0.00 | 0.01 | 0.04 |
| P3H1 | ENSG00000117385 | 0.00 | 0.02 | 0.01 | 0.03 | 0.00 | 0.00 | 0.00 | 0.02 | 0.19 | 0.03 | 0.00 | 0.00 | 0.08 | 0.03 | 0.11 | 0.02 | 0.10 | 0.02 | 0.08 | 0.01 | 0.13 | 0.04 | 0.05 | 0.03 | 0.04 | 0.01 | 0.02 | 0.01 | 0.06 | 0.00 | 0.02 | 0.09 | 0.00 | 0.22 | 0.00 | 0.03 | 0.02 | 0.08 | 0.00 | 0.00 | 0.11 | 0.04 | 0.62 | 0.05 | 0.10 | 0.01 | 0.12 | 0.01 | 0.13 | 0.05 | 0.12 | 0.04 | 0.05 | 0.03 | 0.02 | 0.00 | 0.00 | 0.05 | 0.00 | 0.01 | 0.02 | 0.01 | 0.00 | 0.07 | 0.05 | 0.02 |
| HAPLN2 | ENSG00000132702 | 0.03 | 0.00 | 0.01 | 0.01 | 0.00 | 0.03 | 0.01 | 0.03 | 0.32 | 0.01 | 0.02 | 0.00 | 0.11 | 0.00 | 0.31 | 0.00 | 0.24 | 0.00 | 0.05 | 0.01 | 0.25 | 0.00 | 0.14 | 0.00 | 0.03 | 0.00 | 0.11 | 0.00 | 0.07 | 0.00 | 0.32 | 0.00 | 0.48 | 0.01 | 0.09 | 0.02 | 0.06 | 0.00 | 0.00 | 0.00 | 0.27 | 0.01 | 0.44 | 0.02 | 0.16 | 0.00 | 0.18 | 0.00 | 0.45 | 0.01 | 0.35 | 0.01 | 0.10 | 0.00 | 0.00 | 0.00 | 0.25 | 0.00 | 0.05 | 0.00 | 0.06 | 0.00 | 0.00 | 0.00 | 0.16 | 0.01 |
| CYP27B1 | ENSG00000111012 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.11 | 0.03 | 0.00 | 0.00 | 0.02 | 0.02 | 0.33 | 0.00 | 0.08 | 0.01 | 0.04 | 0.02 | 0.11 | 0.04 | 0.18 | 0.01 | 0.01 | 0.00 | 0.04 | 0.01 | 0.04 | 0.01 | 0.09 | 0.01 | 0.31 | 0.01 | 0.44 | 0.02 | 0.07 | 0.00 | 0.00 | 0.00 | 0.14 | 0.03 | 0.16 | 0.05 | 0.03 | 0.00 | 0.02 | 0.01 | 0.10 | 0.05 | 1.69 | 0.07 | 0.00 | 0.00 | 0.00 | 0.00 | 0.12 | 0.00 | 0.38 | 0.01 | 1.21 | 0.01 | 0.00 | 0.00 | 0.28 | 0.03 |
| SPON2 | ENSG00000159674 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.04 | 0.02 | 0.12 | 0.05 | 0.02 | 0.02 | 0.01 | 0.03 | 0.06 | 0.05 | 0.06 | 0.06 | 0.03 | 0.07 | 0.10 | 0.09 | 0.09 | 0.05 | 0.02 | 0.03 | 0.05 | 0.04 | 0.10 | 0.02 | 0.04 | 0.07 | 0.00 | 0.01 | 0.21 | 0.03 | 0.00 | 0.00 | 0.01 | 0.00 | 0.05 | 0.08 | 0.43 | 0.11 | 0.02 | 0.06 | 0.07 | 0.06 | 0.31 | 0.03 | 0.14 | 0.06 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.02 | 0.01 | 0.04 | 0.02 | 0.00 | 0.05 | 0.05 |
| ADGRB2 | ENSG00000121753 | 0.00 | 0.04 | 0.00 | 0.06 | 0.00 | 0.00 | 0.03 | 0.02 | 0.04 | 0.07 | 0.00 | 0.01 | 0.11 | 0.07 | 0.05 | 0.04 | 0.05 | 0.06 | 0.04 | 0.05 | 0.08 | 0.07 | 0.04 | 0.07 | 0.02 | 0.10 | 0.01 | 0.13 | 0.02 | 0.03 | 0.00 | 0.19 | 0.00 | 0.70 | 0.00 | 0.03 | 0.03 | 0.07 | 0.00 | 0.00 | 0.06 | 0.10 | 0.24 | 0.25 | 0.05 | 0.03 | 0.10 | 0.08 | 0.21 | 0.06 | 0.12 | 0.06 | 0.03 | 0.03 | 0.02 | 0.00 | 0.00 | 0.07 | 0.00 | 0.01 | 0.03 | 0.04 | 0.00 | 0.07 | 0.06 | 0.05 |
| CD69 | ENSG00000110848 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.11 | 0.07 | 0.05 | 0.01 | 0.00 | 0.00 | 0.05 | 0.03 | 0.09 | 0.12 | 0.01 | 0.10 | 0.03 | 0.08 | 0.02 | 0.07 | 0.08 | 0.02 | 0.03 | 0.04 | 0.03 | 0.00 | 0.06 | 0.01 | 0.05 | 0.14 | 0.05 | 0.03 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.09 | 0.05 | 0.35 | 0.09 | 0.01 | 0.02 | 0.04 | 0.03 | 0.16 | 0.03 | 0.13 | 0.13 | 0.56 | 0.00 | 0.00 | 0.01 | 0.00 | 0.08 | 0.10 | 0.01 | 0.03 | 0.05 | 0.00 | 0.01 | 0.04 | 0.03 |
| LOXL1 | ENSG00000129038 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 | 0.02 | 0.00 | 0.03 | 0.04 | 0.02 | 0.00 | 0.00 | 0.09 | 0.00 | 0.05 | 0.01 | 0.05 | 0.01 | 0.02 | 0.02 | 0.07 | 0.03 | 0.05 | 0.03 | 0.02 | 0.01 | 0.03 | 0.03 | 0.03 | 0.01 | 0.04 | 0.03 | 0.00 | 0.01 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.08 | 0.03 | 0.16 | 0.12 | 0.12 | 0.01 | 0.03 | 0.04 | 0.28 | 0.03 | 0.05 | 0.10 | 0.01 | 0.01 | 0.01 | 0.00 | 0.06 | 0.00 | 0.01 | 0.01 | 0.02 | 0.02 | 0.00 | 0.00 | 0.13 | 0.01 |
| GRM3 | ENSG00000198822 | 0.01 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.04 | 0.01 | 0.05 | 0.01 | 0.00 | 0.00 | 0.03 | 0.02 | 0.05 | 0.02 | 0.20 | 0.02 | 0.15 | 0.01 | 0.42 | 0.02 | 0.19 | 0.01 | 0.03 | 0.01 | 0.01 | 0.01 | 0.06 | 0.02 | 0.03 | 0.01 | 0.06 | 0.01 | 0.03 | 0.01 | 0.00 | 0.02 | 0.00 | 0.00 | 0.07 | 0.02 | 0.17 | 0.05 | 0.08 | 0.01 | 0.02 | 0.02 | 0.09 | 0.03 | 0.07 | 0.04 | 0.13 | 0.00 | 0.00 | 0.00 | 0.13 | 0.00 | 0.02 | 0.00 | 0.05 | 0.01 | 0.00 | 0.00 | 0.03 | 0.02 |
| TCIRG1 | ENSG00000110719 | 0.01 | 0.00 | 0.03 | 0.01 | 0.08 | 0.02 | 0.10 | 0.00 | 0.28 | 0.01 | 0.00 | 0.00 | 0.08 | 0.00 | 0.15 | 0.01 | 0.21 | 0.02 | 0.41 | 0.02 | 0.63 | 0.02 | 0.13 | 0.03 | 0.02 | 0.01 | 0.05 | 0.02 | 0.03 | 0.01 | 0.18 | 0.02 | 0.19 | 0.01 | 0.03 | 0.03 | 0.03 | 0.00 | 0.00 | 0.00 | 0.47 | 0.03 | 0.31 | 0.02 | 0.17 | 0.01 | 0.17 | 0.02 | 0.19 | 0.04 | 0.10 | 0.03 | 0.00 | 0.05 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.01 | 0.02 | 0.04 | 0.00 | 0.00 | 0.25 | 0.02 |
| NRBP1 | ENSG00000115216 | 0.00 | 0.00 | 0.04 | 0.01 | 0.00 | 0.00 | 0.01 | 0.01 | 0.08 | 0.01 | 0.00 | 0.00 | 0.03 | 0.07 | 0.06 | 0.01 | 0.10 | 0.01 | 0.03 | 0.01 | 0.04 | 0.05 | 0.03 | 0.03 | 0.00 | 0.00 | 0.02 | 0.02 | 0.01 | 0.04 | 0.09 | 0.00 | 0.00 | 0.05 | 0.05 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.03 | 0.24 | 0.07 | 0.08 | 0.00 | 0.13 | 0.01 | 0.25 | 0.00 | 0.05 | 0.08 | 0.17 | 0.01 | 0.00 | 0.00 | 0.02 | 0.02 | 0.01 | 0.00 | 0.01 | 0.02 | 0.05 | 0.00 | 0.02 | 0.03 |
| TPCN2 | ENSG00000162341 | 0.01 | 0.00 | 0.03 | 0.01 | 0.08 | 0.02 | 0.09 | 0.00 | 0.56 | 0.02 | 0.00 | 0.00 | 0.08 | 0.00 | 0.21 | 0.01 | 0.77 | 0.01 | 1.29 | 0.01 | 2.02 | 0.02 | 0.27 | 0.03 | 0.02 | 0.02 | 0.07 | 0.02 | 0.04 | 0.01 | 0.42 | 0.01 | 0.69 | 0.05 | 0.00 | 0.01 | 0.03 | 0.00 | 0.00 | 0.00 | 0.91 | 0.02 | 0.38 | 0.04 | 0.23 | 0.01 | 0.12 | 0.02 | 0.33 | 0.06 | 0.20 | 0.05 | 0.00 | 0.05 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.01 | 0.01 | 0.03 | 0.00 | 0.00 | 0.35 | 0.02 |
| TNFAIP6 | ENSG00000123610 | 0.01 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.12 | 0.04 | 0.05 | 0.00 | 0.01 | 0.02 | 0.01 | 0.03 | 0.01 | 0.05 | 0.03 | 0.03 | 0.01 | 0.07 | 0.03 | 0.02 | 0.04 | 0.00 | 0.02 | 0.00 | 0.01 | 0.02 | 0.02 | 0.03 | 0.08 | 0.00 | 0.05 | 0.02 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.05 | 0.19 | 0.07 | 0.04 | 0.01 | 0.04 | 0.01 | 0.01 | 0.00 | 0.06 | 0.06 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.16 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 |
| KCNK13 | ENSG00000152315 | 0.00 | 0.02 | 0.01 | 0.00 | 0.00 | 0.04 | 0.02 | 0.05 | 0.06 | 0.05 | 0.00 | 0.00 | 0.00 | 0.05 | 0.07 | 0.05 | 0.11 | 0.02 | 0.04 | 0.05 | 0.08 | 0.06 | 0.02 | 0.04 | 0.00 | 0.03 | 0.01 | 0.02 | 0.01 | 0.01 | 0.02 | 0.09 | 0.00 | 0.40 | 0.05 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.04 | 0.09 | 0.19 | 0.16 | 0.07 | 0.07 | 0.05 | 0.01 | 0.08 | 0.05 | 0.05 | 0.11 | 0.03 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.10 | 0.02 | 0.06 | 0.03 | 0.01 | 0.01 | 0.06 |
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