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 
solute carrier organic anion transporter family member 3A1ENSG00000176463SLCO3A1chr15:91853695-92172435:+                          0.18                                                                                                                                                                                                                                              
FES proto-oncogene, tyrosine kinaseENSG00000182511FESchr15:90883695-90895776:+                          0.18                                                                                                                                                                                                                                              
pecanex 3ENSG00000197136PCNXL3chr11:65615773-65637439:+                                                          0.18                                                                                                                                                                                                              
proline rich and Gla domain 1ENSG00000130962PRRG1chrX:37349275-37457295:+                                                                                                                                                                                                  0.18                                                                      
YES proto-oncogene 1, Src family tyrosine kinaseENSG00000176105YES1chr18:721588-812546:-                                                                                                                                          0.18                                                            0.12                                                                  
transient receptor potential cation channel subfamily A member 1ENSG00000104321TRPA1chr8:72019917-72075617:-                                                                                                                                                                                                  0.18                                                                      
myogenesis regulating glycosidase (putative)ENSG00000164976KIAA1161chr9:34366670-34376853:-                                                                                                                                                                                                                  0.18                                                      
reticulon 4 receptorENSG00000040608RTN4Rchr22:20241415-20283246:-                                                                                                                                          0.17                                                                                                                              
seizure related 6 homolog like 2ENSG00000174938SEZ6L2chr16:29871159-29899547:-          0.17                                                                                                                                                                                                                                                              
transmembrane protein 219ENSG00000149932TMEM219chr16:29940885-29973052:+          0.17                                                                                                                                                                                                                                                              
dynein cytoplasmic 2 heavy chain 1ENSG00000187240DYNC2H1chr11:103109431-103479863:+                                                          0.17                                                                                                                                            0.16                                                        0.3          
proline rich transmembrane protein 2ENSG00000167371PRRT2chr16:29811382-29815892:+          0.17                                                                                                                                                                                                                                                              
CDP-diacylglycerol--inositol 3-phosphatidyltransferaseENSG00000103502CDIPTchr16:29858357-29863736:-          0.17                                                                                                                                                                                                                                                              
solute carrier family 22 member 23ENSG00000137266SLC22A23chr6:3268962-3457022:-                                                                                                                          0.17                                                                            0.14                                                                  
ATPase 13A3ENSG00000133657ATP13A3chr3:194402672-194498364:-          0.17                                                                                                                                                                                            0.11                                                                  
glutamate ionotropic receptor NMDA type subunit 1ENSG00000176884GRIN1chr9:137138390-137168762:+                                                                                                                                                                                                                  0.17                                                      
leucine rich repeat containing 37 member A3ENSG00000176809LRRC37A3chr17:64854312-64919480:-                                                                                                                                                                                                  0.17                                                                      
ADAM metallopeptidase domain 17ENSG00000151694ADAM17chr2:9488486-9555792:-          0.17                                                                                                                                                    0.16                                                                                                          
amnion associated transmembrane proteinENSG00000166126AMNchr14:102922656-102933596:+                                                                                                                                          0.17                                                                                                                              
cadherin 3ENSG00000062038CDH3chr16:68636189-68722616:+          0.17                                                                                                                                                    0.35                                                                                                          

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