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 |
| protocadherin beta 6 | ENSG00000113211 | PCDHB6 | chr5:141150022-141153287:+ | 0.29 | 0.14 | 1 | 1 |
| protocadherin beta 7 | ENSG00000113212 | PCDHB7 | chr5:141172619-141176383:+ | 0.29 | 0.14 | 1 | 1 |
| protocadherin beta 8 | ENSG00000120322 | PCDHB8 | chr5:141177790-141180529:+ | 0.29 | 0.14 | 1 | 1 |
| protocadherin beta 16 | ENSG00000272674 | PCDHB16 | chr5:141181399-141186399:+ | 0.29 | 0.14 | 1 | 1 |
| catenin alpha 1 | ENSG00000044115 | CTNNA1 | chr5:138610967-138935034:+ | 0.29 | 0.13 | 1 | 1 |
| solute carrier family 23 member 1 | ENSG00000170482 | SLC23A1 | chr5:139367196-139384553:- | 0.29 | 0 | 1 | 0 |
| syndecan 1 | ENSG00000115884 | SDC1 | chr2:20200797-20225433:- | 0.29 | 0.15 | 2 | 1 |
| syndecan binding protein 2 | ENSG00000125775 | SDCBP2 | chr20:1309909-1329239:- | 0.29 | 0 | 1 | 0 |
| solute carrier family 7 member 4 | ENSG00000099960 | SLC7A4 | chr22:21028718-21032840:- | 0.29 | 0 | 1 | 0 |
| Bardet-Biedl syndrome 1 | ENSG00000174483 | BBS1 | chr11:66510606-66533627:+ | 0.29 | 0 | 1 | 0 |
| fibroblast growth factor receptor 2 | ENSG00000066468 | FGFR2 | chr10:121478334-121598458:- | 0.29 | 0.19 | 1 | 1 |
| potassium calcium-activated channel subfamily M regulatory beta subunit 4 | ENSG00000135643 | KCNMB4 | chr12:70366276-70434292:+ | 0.28 | 0 | 1 | 0 |
| neuropeptide Y receptor Y6 (pseudogene) | ENSG00000226306 | NPY6R | chr5:137801193-137810751:+ | 0.28 | 0 | 1 | 0 |
| low density lipoprotein receptor class A domain containing 3 | ENSG00000179241 | LDLRAD3 | chr11:35943981-36232136:+ | 0.28 | 0 | 2 | 0 |
| CDC42 small effector 2 | ENSG00000158985 | CDC42SE2 | chr5:131245493-131398447:+ | 0.28 | 0.11 | 1 | 1 |
| solute carrier family 22 member 5 | ENSG00000197375 | SLC22A5 | chr5:132369752-132395614:+ | 0.28 | 0.1 | 1 | 1 |
| solute carrier family 22 member 4 | ENSG00000197208 | SLC22A4 | chr5:132294443-132344206:+ | 0.28 | 0 | 1 | 0 |
| ATP binding cassette subfamily A member 2 | ENSG00000107331 | ABCA2 | chr9:137007227-137028922:- | 0.28 | 0.52 | 2 | 3 |
| thioredoxin domain containing 15 | ENSG00000113621 | TXNDC15 | chr5:134873803-134901525:+ | 0.28 | 0 | 1 | 0 |
| solute carrier family 22 member 17 | ENSG00000092096 | SLC22A17 | chr14:23346306-23352912:- | 0.28 | 0 | 1 | 0 |
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