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 
protocadherin gamma subfamily B, 4ENSG00000253953PCDHGB4chr5:141387698-141512979:+  0    0.15    0    1  
protocadherin gamma subfamily A, 12ENSG00000253159PCDHGA12chr5:141430589-141512979:+  0    0.15    0    1  
protocadherin gamma subfamily A, 2ENSG00000081853PCDHGA2chr5:141338760-141512979:+  0    0.15    0    1  
protocadherin gamma subfamily A, 3ENSG00000254245PCDHGA3chr5:141343829-141512979:+  0    0.15    0    1  
protocadherin gamma subfamily A, 7ENSG00000253537PCDHGA7chr5:141382739-141512979:+  0    0.15    0    1  
protocadherin gamma subfamily A, 11ENSG00000253873PCDHGA11chr5:141421047-141512979:+  0    0.15    0    1  
protocadherin gamma subfamily A, 4ENSG00000262576PCDHGA4chr5:141355025-141512979:+  0    0.15    0    1  
amyloid beta precursor proteinENSG00000142192APPchr21:25880550-26171128:-  0    0.15    0    1  
C-C motif chemokine receptor 6ENSG00000112486CCR6chr6:167111807-167139696:+  0    0.15    0    1  
solute carrier family 16 member 11ENSG00000174326SLC16A11chr17:7041630-7043923:-  0    0.15    0    1  
asialoglycoprotein receptor 1ENSG00000141505ASGR1chr17:7173431-7179564:-  0    0.15    0    1  
asialoglycoprotein receptor 2ENSG00000161944ASGR2chr17:7101322-7115700:-  0    0.15    0    1  
discs large MAGUK scaffold protein 4ENSG00000132535DLG4chr17:7189890-7219702:-  0    0.15    0    1  
protocadherin 17ENSG00000118946PCDH17chr13:57631810-57729311:+  0    0.15    0    1  
integrin alpha FG-GAP repeat containing 1ENSG00000129636ITFG1chr16:47154387-47464149:-  0    0.14    0    1  
TLC domain containing 3AENSG00000167695FAM57Achr17:732412-742972:+  0    0.14    0    1  
interleukin 20 receptor subunit alphaENSG00000016402IL20RAchr6:136999971-137045180:-  0    0.14    0    1  
immunoglobulin superfamily member 3ENSG00000143061IGSF3chr1:116574399-116667755:-  0    0.14    0    1  
calcyon neuron specific vesicular proteinENSG00000130643CALYchr10:133324072-133336935:-  0    0.14    0    1  
solute carrier family 17 member 5ENSG00000119899SLC17A5chr6:73593379-73654155:-  0    0.14    0    1  

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