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 
cell adhesion molecule L1 likeENSG00000134121CHL1chr3:196596-409417:+                                                                                                                                                              0.28                                                                                                          
CD177 moleculeENSG00000204936CD177chr19:43353659-43363172:+                                                                                                                                                              0.28                                                                                                          
gamma-aminobutyric acid type A receptor subunit deltaENSG00000187730GABRDchr1:2019324-2030751:+                                                                                                                                                                                                      0.28                                                                  
ATPase secretory pathway Ca2+ transporting 2ENSG00000064270ATP2C2chr16:84368527-84464187:+                                                                                                                                                                                      0.28                                                                                  
tight junction protein 3ENSG00000105289TJP3chr19:3708109-3750813:+                                                                                                                                                                                                                                                      0.28                  
LY6/PLAUR domain containing 3ENSG00000124466LYPD3chr19:43460787-43465660:-                                                                                                                                                              0.27                                                                                                          
solute carrier family 15 member 4ENSG00000139370SLC15A4chr12:128793191-128823983:-                                                                                                                              0.11                                                                                                                                0.16          
serine incorporator 1ENSG00000111897SERINC1chr6:122443354-122471822:-                                                                                                                                                      0.14                                                        0.12                                                          
frizzled class receptor 3ENSG00000104290FZD3chr8:28494205-28574268:+              0.1                                                                                                                                                                                0.16                                                                          
FYN proto-oncogene, Src family tyrosine kinaseENSG00000010810FYNchr6:111660332-111873452:-              0.12                                                                                                                                                                                                0.14                                                          
teneurin transmembrane protein 3ENSG00000218336TENM3chr4:182143987-182803024:+                      0.12                                                        0.13                                                                                                                                                                                          
golgi glycoprotein 1ENSG00000090863GLG1chr16:74447427-74607144:-                                                                                                                                                                                                                                                              0.25          
protein O-mannosyltransferase 1ENSG00000130714POMT1chr9:131502902-131523806:+                                                                                                                                                              0.25                                                                                                          
tumor suppressor candidate 3ENSG00000104723TUSC3chr8:15417215-15766649:+              0.14                                                                                                                0.11                                                                                                                                          
olfactomedin 1ENSG00000130558OLFM1chr9:135075243-135121179:+                                                                                                                                                              0.25                                                                                                          
LysM domain containing 3ENSG00000176018LYSMD3chr5:90515611-90529584:-                                                              0.12                                                                                                                                                        0.12                                                  
protein kinase C etaENSG00000027075PRKCHchr14:61187559-61550976:+                                                                                                                                                              0.25                                                                                                          
presenilin 2ENSG00000143801PSEN2chr1:226870184-226896105:+                                                                                                                                                                                                      0.25                                                                  
solute carrier family 2 member 6ENSG00000160326SLC2A6chr9:133471095-133479137:-                                                                                                                                                              0.25                                                                                                          
utrophinENSG00000152818UTRNchr6:144285701-144853034:+                                                                      0.11                                                                                                                                        0.14                                                          

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