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).

 

Summary of the G-score 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 
adenylate cyclase 3ENSG00000138031ADCY3chr2:24819169-24919839:-                                                                                                                                                                                                                          0.17                                              
all-trans retinoic acid induced differentiation factorENSG00000138085ATRAIDchr2:27212027-27217178:+                                                                                                                                                                                                                          0.17                                              
solute carrier family 5 member 6ENSG00000138074SLC5A6chr2:27199587-27212958:-                                                                                                                                                                                                                          0.17                                              
fibronectin type III domain containing 4ENSG00000115226FNDC4chr2:27491883-27495245:-                                                                                                                                                                                                                          0.17                                              
dipeptidyl peptidase 7ENSG00000176978DPP7chr9:137110542-137115177:-                                                                                                                                                              0.21                                        0.17            0.17                                            0.14          
multiple EGF like domains 8ENSG00000105429MEGF8chr19:42325609-42378769:+  0.17                                                                                                                                                            0.27                                                                                                0.17          
transmembrane protein 145ENSG00000167619TMEM145chr19:42313325-42325062:+  0.17                                                                                                                                                                                                                                                                      
protein tyrosine phosphatase receptor type HENSG00000080031PTPRHchr19:55181248-55209506:-                  0.17                                                                                                                                                                                                                                                      
myotubularin 1ENSG00000171100MTM1chrX:150568619-150673322:+                                                                                                                                                                                                                  0.17                                                      
leucine rich repeat containing 26ENSG00000184709LRRC26chr9:137168758-137170051:-                                                                                                                                                              0.21                                                    0.17                                                      
claudin 1ENSG00000163347CLDN1chr3:190305701-190322475:-          0.17                                                                                                                                                                                                                                                              
claudin 16ENSG00000113946CLDN16chr3:190322541-190412143:+          0.17                                                                                                                                                                                                                                                              
oxoeicosanoid receptor 1ENSG00000162881OXER1chr2:42762481-42764261:-                                                                                                                                                                                                                          0.17                                              
heat shock protein 90 alpha family class A member 1ENSG00000080824HSP90AA1chr14:102080738-102139699:-                                      0.31                                                                                                    0.17                                                                                                                              
extracellular leucine rich repeat and fibronectin type III domain containing 1ENSG00000225968ELFN1chr7:1688119-1747954:+                                                                                                                                                                                                          0.17                                                              
cingulinENSG00000143375CGNchr1:151510510-151538692:+                                                                                                                                                                                          0.17                                                                              
lin-7 homolog C, crumbs cell polarity complex componentENSG00000148943LIN7Cchr11:27494576-27506773:-                                                          0.16                                                                                                                                                                                                    0.12          
fibronectin leucine rich transmembrane protein 3ENSG00000125848FLRT3chr20:14322988-14337616:-                                              0.27                                                                                                                                            0.16    0.42                        0.29                                                  
cadherin 1ENSG00000039068CDH1chr16:68737225-68835548:+          0.16                                                                                                                                                    0.35                                                                                                          
interleukin 11 receptor subunit alphaENSG00000137070IL11RAchr9:34650702-34661892:+                                                                                                                                                                                                                  0.16                                                      

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