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 9 superfamily member 2ENSG00000125304TM9SF2chr13:99501417-99564006:+                  1        1                                                                                                1        1                                                                                                                                      
CD72 moleculeENSG00000137101CD72chr9:35609533-35646810:-                                                                          1                                                                1                                                                                                                              
protein kinase C alphaENSG00000154229PRKCAchr17:66302636-66810743:+                                          1                                                                                                                                                1        1        1                                                              
notch receptor 2ENSG00000134250NOTCH2chr1:119911553-120069626:-                                                          1                    1                                                            1                                                                1                                                              
transmembrane protein 67ENSG00000164953TMEM67chr8:93754844-93819234:+                                                                                                                                                                                                  1                        1                                        1      
dpy-19 like 4ENSG00000156162DPY19L4chr8:94719703-94793836:+                                                                                                                                                                                                  1                        1                                        1      
dual specificity phosphatase 15ENSG00000149599DUSP15chr20:31847637-31870747:-                                          1                                                                                                1                                                1                                                                              
zinc activated ion channelENSG00000186919ZACNchr17:76071961-76083666:+          1                1                                                                                                                1                                                                                                                              
transmembrane protein 64ENSG00000180694TMEM64chr8:90621995-90791632:-                                                                                                                                                                                                  1                        1                                        1      
potassium calcium-activated channel subfamily M regulatory beta subunit 3ENSG00000171121KCNMB3chr3:179236691-179267002:-          1        1                                                                                                                                                                                                        1                                              
exocyst complex component 1ENSG00000090989EXOC1chr4:55853616-55905034:+                                                                                                                                  1                                                                1                        1                                              
ATP binding cassette subfamily A member 5ENSG00000154265ABCA5chr17:69244311-69327244:-          1                                                                                                                                1                                                                1                                                              
ethanolamine kinase 1ENSG00000139163ETNK1chr12:22625075-22690665:+                                                                                                                                                                                                                          1                                              
T cell immune regulator 1, ATPase H+ transporting V0 subunit a3ENSG00000110719TCIRG1chr11:68039016-68050895:+                                                          1                                                                                                                                                                                                              
ATP binding cassette subfamily C member 9ENSG00000069431ABCC9chr12:21797401-21941402:-                                                                                                                                                                                                                          1                                              
peripheral myelin protein 22ENSG00000109099PMP22chr17:15229777-15265326:-                                                                                                                                                                                                  1                                                                      
ADAM metallopeptidase domain 15ENSG00000143537ADAM15chr1:155050566-155062775:+                          1                                1                                                                                                                                                1                                                              
WW domain containing E3 ubiquitin protein ligase 1ENSG00000123124WWP1chr8:86342738-86478420:+                                                                                                                                                                                                  1                        1                                        1      
calsyntenin 3ENSG00000139182CLSTN3chr12:7129698-7158945:+                                                                                                                                                                                                                          1                                              
glyceraldehyde-3-phosphate dehydrogenaseENSG00000111640GAPDHchr12:6533927-6538374:+                                                                                                                                                                                                                          1                                              

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