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 |
| membrane magnesium transporter 1 | ENSG00000169446 | MMGT1 | chrX:135962070-135974063:- | 0.13 | 0 | 1 | 0 |
| integrin subunit beta 1 | ENSG00000150093 | ITGB1 | chr10:32900319-33005792:- | 0.13 | 0 | 1 | 0 |
| cholinergic receptor nicotinic beta 4 subunit | ENSG00000117971 | CHRNB4 | chr15:78624119-78727754:- | 0.13 | 0 | 1 | 0 |
| KIT proto-oncogene, receptor tyrosine kinase | ENSG00000157404 | KIT | chr4:54657918-54740715:+ | 0.13 | 0 | 1 | 0 |
| zinc finger DHHC-type palmitoyltransferase 5 | ENSG00000156599 | ZDHHC5 | chr11:57667747-57701187:+ | 0.13 | 0.11 | 1 | 1 |
| major facilitator superfamily domain containing 6 | ENSG00000151690 | MFSD6 | chr2:190408355-190509205:+ | 0.13 | 0 | 1 | 0 |
| endosome-lysosome associated apoptosis and autophagy regulator family member 2 | ENSG00000164659 | KIAA1324L | chr7:86876906-87059699:- | 0.13 | 0 | 1 | 0 |
| cysteine rich transmembrane BMP regulator 1 | ENSG00000150938 | CRIM1 | chr2:36355926-36551135:+ | 0.13 | 0 | 1 | 0 |
| major facilitator superfamily domain containing 12 | ENSG00000161091 | MFSD12 | chr19:3538261-3574290:- | 0.13 | 1.2 | 1 | 3 |
| adaptor related protein complex 2 subunit sigma 1 | ENSG00000042753 | AP2S1 | chr19:46838136-46850992:- | 0.13 | 0.52 | 1 | 2 |
| solute carrier family 8 member A2 | ENSG00000118160 | SLC8A2 | chr19:47428017-47472168:- | 0.13 | 0 | 1 | 0 |
| integrin subunit beta 8 | ENSG00000105855 | ITGB8 | chr7:20330702-20415754:+ | 0.13 | 0 | 1 | 0 |
| plexin A4 | ENSG00000221866 | PLXNA4 | chr7:132123332-132648688:- | 0.13 | 0 | 1 | 0 |
| epithelial cell adhesion molecule | ENSG00000119888 | EPCAM | chr2:47345158-47387601:+ | 0.13 | 0 | 1 | 0 |
| cholinergic receptor nicotinic alpha 5 subunit | ENSG00000169684 | CHRNA5 | chr15:78565520-78595269:+ | 0.12 | 0 | 1 | 0 |
| syndecan 4 | ENSG00000124145 | SDC4 | chr20:45325288-45348424:- | 0.12 | 0 | 1 | 0 |
| pannexin 1 | ENSG00000110218 | PANX1 | chr11:94128928-94181972:+ | 0.12 | 0.16 | 1 | 1 |
| integrin subunit alpha V | ENSG00000138448 | ITGAV | chr2:186590065-186680901:+ | 0.12 | 0.16 | 1 | 1 |
| neuregulin 4 | ENSG00000169752 | NRG4 | chr15:75935969-76059795:- | 0.12 | 0 | 1 | 0 |
| transmembrane protein 266 | ENSG00000169758 | C15orf27 | chr15:76059837-76229121:+ | 0.12 | 0 | 1 | 0 |
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