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 
NCK associated protein 1ENSG00000061676NCKAP1chr2:182909115-183038858:-                          0.12                                                                                                                                                                                                                                              
syntaxin 1AENSG00000106089STX1Achr7:73699206-73719672:-                                                                                                                                                                                                                          0.12                                              
KIAA1549ENSG00000122778KIAA1549chr7:138831381-138981318:-                                                                                                                  0.12                                                                                                                                                      
kinase insert domain receptorENSG00000128052KDRchr4:55078477-55125589:-                                                                                                                                  0.12                                                                                                                                      
ribitol xylosyltransferase 1ENSG00000118600TMEM5chr12:63779803-63809558:+                                                  0.12                                                                                                                                                                                                                      
retinal outer segment membrane protein 1ENSG00000149489ROM1chr11:62611722-62615120:+                                                          0.12                                                                                                                                                                                                    0.12          
CD46 moleculeENSG00000117335CD46chr1:207752057-207795513:+                                                                                                                                                                                          0.12                                                                              
plexin A2ENSG00000076356PLXNA2chr1:208022242-208244320:-                                                                                                                                                                                          0.12                                                                              
G protein-coupled receptor 155ENSG00000163328GPR155chr2:174431571-174487094:-                          0.12                                                                                                                                                                                                                                              
microtubule affinity regulating kinase 2ENSG00000072518MARK2chr11:63838928-63911019:+                                                          0.12                                                                                                                                                                                                    0.16          
solute carrier family 41 member 1ENSG00000133065SLC41A1chr1:205789093-205813748:-                                                                                                                                                                                          0.12                                                                              
ADP ribosylation factor 6ENSG00000165527ARF6chr14:49893092-49897054:+                                                                                                                                                                                                                  0.12                                                      
beta-secretase 2ENSG00000182240BACE2chr21:41167801-41282518:+                                                                                                          0.12                                                    0.16                                                                                                          
CD276 moleculeENSG00000103855CD276chr15:73683966-73714518:+                          0.12                                                                                                                                                                                                                                              
solute carrier family 3 member 1ENSG00000138079SLC3A1chr2:44275458-44321494:+                                                                                                                                                                                                                          0.12                                              
beta-1,4-galactosyltransferase 5ENSG00000158470B4GALT5chr20:49632945-49713878:-                                                                                                                                                                                          0.12                                                                              
proline rich transmembrane protein 4ENSG00000224940PRRT4chr7:128350325-128361685:-                                                                                                                  0.12                                                                                                                                                      
sulfatase 2ENSG00000196562SULF2chr20:47656348-47786616:-                                                                                                                                                                                          0.12                                                                              
solute carrier family 38 member 7ENSG00000103042SLC38A7chr16:58665109-58685104:-                                                                                                                                                                                                                          0.12                                    0.16          
glutamic-oxaloacetic transaminase 2ENSG00000125166GOT2chr16:58707131-58734357:-                                                                                                                                                                                                                          0.12                                    0.16          

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