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).

 

List of the putative cancer-causing GESPs driven by SCNAs in each cancer type


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

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