Copy Number
The putative cancer-associated GESPs 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 Name | Ensembl Gene ID | HGNC Symbol | Genomic Location | Amplification | Deletion | Amplification | Deletion |
| G protein-coupled receptor 162 | ENSG00000250510 | GPR162 | chr12:6821545-6829972:+ | 0.6 | 0 | 1 | 0 |
| pyrimidinergic receptor P2Y6 | ENSG00000171631 | P2RY6 | chr11:73264505-73298617:+ | 0.6 | 0 | 1 | 0 |
| tweety family member 2 | ENSG00000141540 | TTYH2 | chr17:74213514-74262020:+ | 0.6 | 0 | 3 | 0 |
| RELT TNF receptor | ENSG00000054967 | RELT | chr11:73376264-73397474:+ | 0.59 | 0 | 1 | 0 |
| TNF receptor superfamily member 1A | ENSG00000067182 | TNFRSF1A | chr12:6328757-6342114:- | 0.58 | 0 | 1 | 0 |
| CD9 molecule | ENSG00000010278 | CD9 | chr12:6199715-6238271:+ | 0.58 | 0 | 1 | 0 |
| sodium channel epithelial 1 subunit alpha | ENSG00000111319 | SCNN1A | chr12:6346843-6377730:- | 0.58 | 0 | 1 | 0 |
| lymphotoxin beta receptor | ENSG00000111321 | LTBR | chr12:6375045-6391571:+ | 0.58 | 0 | 1 | 0 |
| Rac family small GTPase 1 | ENSG00000136238 | RAC1 | chr7:6374523-6403977:+ | 0.58 | 0.39 | 4 | 1 |
| diacylglycerol lipase beta | ENSG00000164535 | DAGLB | chr7:6409126-6484190:- | 0.58 | 0.39 | 4 | 1 |
| phosphatidylinositol 4-kinase alpha | ENSG00000241973 | PI4KA | chr22:20707691-20859417:- | 0.58 | 0 | 2 | 0 |
| synaptosome associated protein 29 | ENSG00000099940 | SNAP29 | chr22:20858983-20891218:+ | 0.58 | 0 | 2 | 0 |
| limb development membrane protein 1 | ENSG00000105983 | LMBR1 | chr7:156668946-156893230:- | 0.58 | 0.44 | 1 | 3 |
| hyaluronan synthase 2 | ENSG00000170961 | HAS2 | chr8:121612116-121641390:- | 0.57 | 0 | 3 | 0 |
| potassium voltage-gated channel subfamily A member 5 | ENSG00000130037 | KCNA5 | chr12:5043989-5046788:+ | 0.57 | 0 | 1 | 0 |
| syndecan 2 | ENSG00000169439 | SDC2 | chr8:96493351-96611780:+ | 0.57 | 0 | 2 | 0 |
| transmembrane 7 superfamily member 3 | ENSG00000064115 | TM7SF3 | chr12:26973195-27014434:- | 0.57 | 0 | 1 | 0 |
| solute carrier family 2 member 3 | ENSG00000059804 | SLC2A3 | chr12:7919230-7936275:- | 0.57 | 0 | 1 | 0 |
| mannose-6-phosphate receptor, cation dependent | ENSG00000003056 | M6PR | chr12:8940363-8949955:- | 0.57 | 0 | 1 | 0 |
| anoctamin 6 | ENSG00000177119 | ANO6 | chr12:45215987-45440404:+ | 0.57 | 0 | 1 | 0 |
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