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 
kringle containing transmembrane protein 1ENSG00000183762KREMEN1chr22:29073078-29168333:+          0.22                                                                                                                                                                                                                                                              
toll like receptor adaptor molecule 2ENSG00000243414TICAM2chr5:115578650-115602479:-                                                                                          0.22                                                                                                                            0.12                                                  
cholinergic receptor nicotinic beta 2 subunitENSG00000160716CHRNB2chr1:154567781-154580026:+                                                                                                                                                                                                          0.22                                                              
ATPase phospholipid transporting 8B2ENSG00000143515ATP8B2chr1:154325553-154351307:+                                                                                                                                                                                                          0.22                                                              
prostaglandin E receptor 4ENSG00000171522PTGER4chr5:40679498-40693735:+                                                                                                                                                                                                                  0.21                                                      
G protein-coupled receptor class C group 5 member CENSG00000170412GPRC5Cchr17:74424851-74451653:+          0.21                                                                                                                                                                                                                                                              
AHNAK nucleoprotein 2ENSG00000185567AHNAK2chr14:104937244-104978357:-                                                                                                                                          0.21                                                                                                                              
LIF receptor subunit alphaENSG00000113594LIFRchr5:38474963-38608354:-                                                                                                                                  0.21                                                                                                                                      
myelin protein zero like 1ENSG00000197965MPZL1chr1:167721192-167791919:+                                                          0.21                                                                                                                                                                                                              
phosphoinositide-3-kinase interacting protein 1ENSG00000100100PIK3IP1chr22:31281593-31292534:-          0.2                                                                                                                                                                                                                                                              
potassium inwardly rectifying channel subfamily J member 2ENSG00000123700KCNJ2chr17:70168673-70180048:+                                                                                                                                          0.2                                                                                                                              
adenylate cyclase 8ENSG00000155897ADCY8chr8:130780301-131042426:-                                                                                                                  0.2                                                                                                                                                      
neuroligin 1ENSG00000169760NLGN1chr3:173396284-174286644:+                                                                                                                                                                                                                          0.2                                              
repulsive guidance molecule BMP co-receptor aENSG00000182175RGMAchr15:93035273-93089204:-                                                                                                                                                                                                          0.2                                                              
leucine rich repeat containing G protein-coupled receptor 4ENSG00000205213LGR4chr11:27365961-27472775:-                                                          0.2                                                                                                                                                                                                              
microtubule affinity regulating kinase 3ENSG00000075413MARK3chr14:103385392-103503831:+                                      0.31                                                                                        0.13            0.2                                                                                                                              
LYN proto-oncogene, Src family tyrosine kinaseENSG00000254087LYNchr8:55879813-56014168:+                                                                                                                                                                                                                                                                  0.2      
phosphatidylinositol binding clathrin assembly proteinENSG00000073921PICALMchr11:85957684-86069882:-                                                          0.19                                                                                                                                                                                                    0.19          
solute carrier family 51 subunit alphaENSG00000163959SLC51Achr3:196211487-196243178:+          0.19                                                                                                                                                                                            0.14                                                                  
mucin 4, cell surface associatedENSG00000145113MUC4chr3:195746765-195812277:-          0.19                                                                                                                                                                                                                                                              

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