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).

 

Pan-cancer level overall G-score of GESPs that recurrently gained or lost copy number in at least one cancer types


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Overall_Gscore No. of Cancer Types
 HGNC Name  Ensembl Gene ID  HGNC Symbol  Genomic Location  Amplification  Deletion  Amplification  Deletion 
transmembrane serine protease 2ENSG00000184012TMPRSS2chr21:41464551-41531116:-  0    0.41    0    1  
cytochrome b-245 alpha chainENSG00000051523CYBAchr16:88643283-88651152:-  0    0.41    0    3  
CD52 moleculeENSG00000169442CD52chr1:26317957-26320523:+  0    0.4    0    3  
roundabout guidance receptor 3ENSG00000154134ROBO3chr11:124865386-124881470:+  0    0.4    0    2  
G protein-coupled estrogen receptor 1ENSG00000164850GPER1chr7:1082208-1093815:+  0    0.4    0    1  
protein tyrosine phosphatase receptor type GENSG00000144724PTPRGchr3:61561569-62297613:+  0    0.4    0    3  
semaphorin 3GENSG00000010319SEMA3Gchr3:52433053-52445085:-  0    0.39    0    2  
matrix remodeling associated 8ENSG00000162576MXRA8chr1:1352689-1361777:-  0    0.39    0    2  
TNF receptor superfamily member 4ENSG00000186827TNFRSF4chr1:1211326-1214138:-  0    0.39    0    2  
serine peptidase inhibitor, Kunitz type 1ENSG00000166145SPINT1chr15:40844018-40858207:+  0    0.39    0    3  
interferon gamma receptor 1ENSG00000027697IFNGR1chr6:137197484-137219449:-  0    0.38    0    3  
ecto-NOX disulfide-thiol exchanger 1ENSG00000120658ENOX1chr13:43213518-43786908:-  0    0.38    0    2  
A-kinase anchoring protein 11ENSG00000023516AKAP11chr13:42272153-42323267:+  0    0.38    0    2  
spectrin repeat containing nuclear envelope protein 2ENSG00000054654SYNE2chr14:63852983-64226433:+  0    0.38    0    2  
FLVCR heme transporter 1ENSG00000162769FLVCR1chr1:212858255-212899363:+  0    0.38    0    2  
EPH receptor A4ENSG00000116106EPHA4chr2:221418027-221574202:-  0    0.37    0    2  
transmembrane protein 30AENSG00000112697TMEM30Achr6:75252924-75284968:-  0    0.37    0    2  
solute carrier family 12 member 6ENSG00000140199SLC12A6chr15:34229996-34338060:-  0    0.37    0    1  
peroxidasinENSG00000130508PXDNchr2:1631887-1744852:-  0    0.37    0    2  
STAM binding protein like 1ENSG00000138134STAMBPL1chr10:88879734-88975153:+  0    0.37    0    2  

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