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 
mucin 20, cell surface associatedENSG00000176945MUC20chr3:195720882-195741123:+          0.19                                                                                                                                                                                                                                                              
potassium voltage-gated channel subfamily Q member 2ENSG00000075043KCNQ2chr20:63400210-63472677:-                                                                                                                                                                                                  0.19                                                                      
milk fat globule EGF and factor V/VIII domain containingENSG00000140545MFGE8chr15:88898683-88913411:-                                                                                                                                                                                                          0.19                                                              
semaphorin 4CENSG00000168758SEMA4Cchr2:96859716-96870757:-                                                                          0.19                                                                                                                                                                                              
lysosomal associated membrane protein 3ENSG00000078081LAMP3chr3:183122213-183163839:-          0.19                                                                                                                                                                                                                                                              
discs large MAGUK scaffold protein 1ENSG00000075711DLG1chr3:197042560-197299300:-          0.19                                                                                                                                                                                            0.12                                                                  
potassium calcium-activated channel subfamily M regulatory beta subunit 2ENSG00000197584KCNMB2chr3:178272932-178844429:+                                                                                                                                                                                                                          0.19                                              
annexin A13ENSG00000104537ANXA13chr8:123680794-123737407:-                                                                                                                                                                                                          0.19                                                              
CUB and Sushi multiple domains 3ENSG00000164796CSMD3chr8:112222928-113437099:-                                                                                                                  0.19                                                                                                                                                      
synaptic vesicle glycoprotein 2BENSG00000185518SV2Bchr15:91099950-91301309:+                                                                                                                                                                                                          0.19                                                              
transmembrane protein 127ENSG00000135956TMEM127chr2:96248516-96265994:-                                                                                                                                                                                                  0.19                                                                      
CD82 moleculeENSG00000085117CD82chr11:44564427-44620363:+                                                          0.19                                                                                                                                                                                                              
interleukin 2 receptor subunit alphaENSG00000134460IL2RAchr10:6010689-6062325:-                  0.19                                                                                                                                                                                                                                                      
interleukin 15 receptor subunit alphaENSG00000134470IL15RAchr10:5937569-5978187:-                  0.19                                                                                                                                                                                                                                                      
kirre like nephrin family adhesion molecule 1ENSG00000183853KIRRELchr1:157993273-158100262:+                                                                                                                                                                                                          0.19                                                              
solute carrier family 9 member A3ENSG00000066230SLC9A3chr5:473310-524332:-                                                                                                                                                                                                                  0.18                                                      
chromosome 19 open reading frame 18ENSG00000177025C19orf18chr19:57958437-57974534:-                  0.18                                                                                                                                                                                                                                                      
symplekinENSG00000125755SYMPKchr19:45815410-45863290:-  0.18                                                                                                                                                            0.3                                                                                                0.19          
cytohesin 2ENSG00000105443CYTH2chr19:48469032-48482314:+  0.18                                                                                                                                                            0.33                                                                                                0.22          
potassium inwardly rectifying channel subfamily J member 14ENSG00000182324KCNJ14chr19:48455509-48466980:+  0.18                                                                                                                                                            0.33                                                                                                          

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