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 |
| MMP25 | ENSG00000008516 | 0.00 | 0.00 | 0 | 0 |
| SCP2 | ENSG00000116171 | 0.00 | 0.00 | 0 | 0 |
| CCRL2 | ENSG00000121797 | 0.00 | 0.00 | 0 | 0 |
| SCN8A | ENSG00000196876 | 0.00 | 0.00 | 0 | 0 |
| P4HA1 | ENSG00000122884 | 0.00 | 0.00 | 0 | 0 |
| RPS6KA6 | ENSG00000072133 | 0.00 | 0.00 | 0 | 0 |
| ADCK3 | ENSG00000163050 | 0.00 | 0.25 | 0 | 1 |
| SIRT3 | ENSG00000142082 | 0.00 | 1.51 | 0 | 7 |
| CTSH | ENSG00000103811 | 0.12 | 0.00 | 1 | 0 |
| TCN2 | ENSG00000185339 | 0.23 | 0.00 | 1 | 0 |
| BMPER | ENSG00000164619 | 0.00 | 0.00 | 0 | 0 |
| CD37 | ENSG00000104894 | 0.00 | 0.00 | 0 | 0 |
| TXNDC11 | ENSG00000153066 | 0.23 | 0.00 | 1 | 0 |
| PSIP1 | ENSG00000164985 | 0.00 | 0.00 | 0 | 0 |
| CYP27A1 | ENSG00000135929 | 0.00 | 0.53 | 0 | 2 |
| PDE1A | ENSG00000115252 | 0.00 | 0.00 | 0 | 0 |
| PLCH2 | ENSG00000149527 | 0.00 | 0.00 | 0 | 0 |
| AGER | ENSG00000204305 | 0.00 | 0.00 | 0 | 0 |
| TMX3 | ENSG00000166479 | 0.10 | 0.56 | 1 | 4 |
| ARNT | ENSG00000143437 | 3.74 | 0.00 | 12 | 0 |
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