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 
transmembrane p24 trafficking protein 10ENSG00000170348TMED10chr14:75131470-75176631:-                      1                1                                                                                1                                                                                                                                                  
transient receptor potential cation channel subfamily M member 4ENSG00000130529TRPM4chr19:49157741-49211836:+                                                                                                                                                              1                                                                                                1          
Fc fragment of IgG receptor and transporterENSG00000104870FCGRTchr19:49506816-49526333:+                                                                                                                                                              1                                                                                                1          
receptor activity modifying protein 1ENSG00000132329RAMP1chr2:237858893-237912114:+              1                                                                                                                                1                                                                                                                          
prostaglandin F2 receptor inhibitorENSG00000134247PTGFRNchr1:116910057-116990358:+                                                                              1                                                        1        1                                                                                                                          
phosphatidylinositol 4-kinase type 2 alphaENSG00000155252PI4K2Achr10:97640686-97676434:+                                                                                                                                                      1        1                                                                                                          
SPG11 vesicle trafficking associated, spatacsinENSG00000104133SPG11chr15:44562696-44663678:-                                                                                                                                                      1                                                        1                                                          
pleckstrin and Sec7 domain containingENSG00000059915PSDchr10:102402617-102421539:-                                                                                                                                                      1        1                                                                                                          
vasodilator stimulated phosphoproteinENSG00000125753VASPchr19:45506579-45526983:+                                                                                                                                                              1                                                                                                1          
heat shock protein family A (Hsp70) member 8ENSG00000109971HSPA8chr11:123057489-123063230:-                              1                                                                                                                                1                                                                                                          
membrane associated guanylate kinase, WW and PDZ domain containing 3ENSG00000081026MAGI3chr1:113390749-113685923:+                                                              1                1                                                        1                                                                                                                                  
zinc finger DHHC-type palmitoyltransferase 20ENSG00000180776ZDHHC20chr13:21372573-21459370:-                              1                                                1                                                                        1                                                                                                                  
sortilin related receptor 1ENSG00000137642SORL1chr11:121452203-121633693:+                              1                                                                                                                                1                                                                                                          
membrane palmitoylated protein 5ENSG00000072415MPP5chr14:67241109-67335819:+                      1                                                                                                1                                        1                                                                                                          
basigin (Ok blood group)ENSG00000172270BSGchr19:571277-583493:+              1                                                1                                                                                1                                                                                                                          
interferon induced transmembrane protein 2ENSG00000185201IFITM2chr11:307631-315272:+                      1                                        1                                                                                                                                                                                                1          
G protein subunit alpha i3ENSG00000065135GNAI3chr1:109548611-109618321:+                                                                                                                                      1                1                                                                                                                  
glycoprotein integral membrane 1ENSG00000055211GINM1chr6:149566294-149591748:+                                      1                                                                                                                1                                                        1                                                          
leucine rich repeats and immunoglobulin like domains 2ENSG00000198799LRIG2chr1:113073209-113132260:+                                                              1                1                                                        1                                                                                                                                  
colony stimulating factor 1ENSG00000184371CSF1chr1:109910242-109930992:+                                                                                                                                      1                1                                                                                                                  

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