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 |
| kringle containing transmembrane protein 1 | ENSG00000183762 | KREMEN1 | chr22:29073078-29168333:+ | 0.22 | 0 | 1 | 0 |
| toll like receptor adaptor molecule 2 | ENSG00000243414 | TICAM2 | chr5:115578650-115602479:- | 0.22 | 0.12 | 1 | 1 |
| cholinergic receptor nicotinic beta 2 subunit | ENSG00000160716 | CHRNB2 | chr1:154567781-154580026:+ | 0.22 | 0 | 1 | 0 |
| ATPase phospholipid transporting 8B2 | ENSG00000143515 | ATP8B2 | chr1:154325553-154351307:+ | 0.22 | 0 | 1 | 0 |
| prostaglandin E receptor 4 | ENSG00000171522 | PTGER4 | chr5:40679498-40693735:+ | 0.21 | 0 | 1 | 0 |
| G protein-coupled receptor class C group 5 member C | ENSG00000170412 | GPRC5C | chr17:74424851-74451653:+ | 0.21 | 0 | 1 | 0 |
| AHNAK nucleoprotein 2 | ENSG00000185567 | AHNAK2 | chr14:104937244-104978357:- | 0.21 | 0 | 1 | 0 |
| LIF receptor subunit alpha | ENSG00000113594 | LIFR | chr5:38474963-38608354:- | 0.21 | 0 | 1 | 0 |
| myelin protein zero like 1 | ENSG00000197965 | MPZL1 | chr1:167721192-167791919:+ | 0.21 | 0 | 1 | 0 |
| phosphoinositide-3-kinase interacting protein 1 | ENSG00000100100 | PIK3IP1 | chr22:31281593-31292534:- | 0.2 | 0 | 1 | 0 |
| potassium inwardly rectifying channel subfamily J member 2 | ENSG00000123700 | KCNJ2 | chr17:70168673-70180048:+ | 0.2 | 0 | 1 | 0 |
| adenylate cyclase 8 | ENSG00000155897 | ADCY8 | chr8:130780301-131042426:- | 0.2 | 0 | 1 | 0 |
| neuroligin 1 | ENSG00000169760 | NLGN1 | chr3:173396284-174286644:+ | 0.2 | 0 | 1 | 0 |
| repulsive guidance molecule BMP co-receptor a | ENSG00000182175 | RGMA | chr15:93035273-93089204:- | 0.2 | 0 | 1 | 0 |
| leucine rich repeat containing G protein-coupled receptor 4 | ENSG00000205213 | LGR4 | chr11:27365961-27472775:- | 0.2 | 0 | 1 | 0 |
| microtubule affinity regulating kinase 3 | ENSG00000075413 | MARK3 | chr14:103385392-103503831:+ | 0.2 | 0.44 | 1 | 2 |
| LYN proto-oncogene, Src family tyrosine kinase | ENSG00000254087 | LYN | chr8:55879813-56014168:+ | 0.2 | 0 | 1 | 0 |
| phosphatidylinositol binding clathrin assembly protein | ENSG00000073921 | PICALM | chr11:85957684-86069882:- | 0.19 | 0.19 | 1 | 1 |
| solute carrier family 51 subunit alpha | ENSG00000163959 | SLC51A | chr3:196211487-196243178:+ | 0.19 | 0.14 | 1 | 1 |
| mucin 4, cell surface associated | ENSG00000145113 | MUC4 | chr3:195746765-195812277:- | 0.19 | 0 | 1 | 0 |
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