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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| Overall_Gscore | No. of Cancer Types | ||||
| HGNC Symbol | Ensembl Gene ID | Amplification | Deletion | Amplification | Deletion |
| CHIT1 | ENSG00000133063 | 0.00 | 0.00 | 0 | 0 |
| RXFP2 | ENSG00000133105 | 0.00 | 0.00 | 0 | 0 |
| MORC4 | ENSG00000133131 | 0.00 | 0.00 | 0 | 0 |
| CNDP2 | ENSG00000133313 | 0.00 | 0.83 | 0 | 4 |
| GSTT2B | ENSG00000133433 | 0.00 | 0.00 | 0 | 0 |
| SLC2A11 | ENSG00000133460 | 0.00 | 0.00 | 0 | 0 |
| GGT2 | ENSG00000133475 | 0.00 | 0.00 | 0 | 0 |
| NTS | ENSG00000133636 | 0.00 | 0.00 | 0 | 0 |
| LARS | ENSG00000133706 | 0.31 | 0.14 | 1 | 1 |
| SARAF | ENSG00000133872 | 0.00 | 0.00 | 0 | 0 |
| DPF2 | ENSG00000133884 | 0.15 | 0.00 | 1 | 0 |
| ADAM20 | ENSG00000134007 | 0.00 | 0.00 | 0 | 0 |
| CCNB1 | ENSG00000134057 | 0.00 | 0.88 | 0 | 2 |
| CD180 | ENSG00000134061 | 0.00 | 0.00 | 0 | 0 |
| CAMK1 | ENSG00000134072 | 0.00 | 0.00 | 0 | 0 |
| CHL1 | ENSG00000134121 | 0.00 | 0.28 | 0 | 1 |
| GSTM1 | ENSG00000134184 | 0.00 | 0.00 | 0 | 0 |
| REG4 | ENSG00000134193 | 0.00 | 0.00 | 0 | 0 |
| TSHB | ENSG00000134200 | 0.00 | 0.00 | 0 | 0 |
| GSTM3 | ENSG00000134202 | 0.00 | 0.13 | 0 | 1 |
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