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 |
| KLHL24 | ENSG00000114796 | 0.19 | 0.00 | 1 | 0 |
| SCMH1 | ENSG00000010803 | 0.13 | 0.00 | 1 | 0 |
| SLC29A1 | ENSG00000112759 | 0.30 | 0.00 | 2 | 0 |
| IFNGR2 | ENSG00000159128 | 0.00 | 0.00 | 0 | 0 |
| SLC6A6 | ENSG00000131389 | 0.00 | 0.00 | 0 | 0 |
| PDGFC | ENSG00000145431 | 0.00 | 0.00 | 0 | 0 |
| CARM1 | ENSG00000142453 | 0.00 | 0.00 | 0 | 0 |
| MMRN2 | ENSG00000173269 | 0.00 | 0.00 | 0 | 0 |
| KITLG | ENSG00000049130 | 0.00 | 0.00 | 0 | 0 |
| TAOK3 | ENSG00000135090 | 0.00 | 0.00 | 0 | 0 |
| CYP2R1 | ENSG00000186104 | 0.00 | 0.00 | 0 | 0 |
| SLC35B3 | ENSG00000124786 | 0.41 | 0.36 | 2 | 2 |
| FRK | ENSG00000111816 | 0.00 | 0.00 | 0 | 0 |
| BTD | ENSG00000169814 | 0.00 | 0.18 | 0 | 1 |
| SERPING1 | ENSG00000149131 | 0.00 | 0.00 | 0 | 0 |
| HIAT1 | ENSG00000156875 | 0.00 | 0.62 | 0 | 3 |
| MAP2K7 | ENSG00000076984 | 0.00 | 0.00 | 0 | 0 |
| CDC42BPB | ENSG00000198752 | 0.17 | 0.12 | 1 | 1 |
| MMP15 | ENSG00000102996 | 0.00 | 0.00 | 0 | 0 |
| RIPK1 | ENSG00000137275 | 0.41 | 0.38 | 2 | 2 |
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