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 
uronyl 2-sulfotransferaseENSG00000111962USTchr6:148747328-149076990:+                                                                                                                                                                                                  0.56            0.13                                                          
extended synaptotagmin 2ENSG00000117868ESYT2chr7:158730995-158830253:-                                                              0.26                                                                                0.11            0.56                                            0.22                                                        0.23          
3'(2'), 5'-bisphosphate nucleotidase 2ENSG00000104331IMPAD1chr8:56957933-56993844:-                                                                                                                                                                                                  0.16                        0.18                                        0.22      
oxidized low density lipoprotein receptor 1ENSG00000173391OLR1chr12:10158301-10172138:-                                                                                                                                                                                                                          0.56                                              
C-type lectin domain family 1 member AENSG00000150048CLEC1Achr12:10069554-10111627:-                                                                                                                                                                                                                          0.56                                              
serine/threonine/tyrosine kinase 1ENSG00000060140STYK1chr12:10618939-10674318:-                                                                                                                                                                                                                          0.56                                              
taste 2 receptor member 14ENSG00000212127TAS2R14chr12:10937406-11171573:-                                                                                                                                                                                                      0.16                    0.55                                              
taste 2 receptor member 19ENSG00000212124TAS2R19chr12:11021619-11022620:-                                                                                                                                                                                                                          0.55                                              
taste 2 receptor member 31ENSG00000256436TAS2R31chr12:11030387-11031407:-                                                                                                                                                                                                                          0.55                                              
vesicle associated membrane protein 7ENSG00000124333VAMP7chrX:155881293-155943769:+                          0.24                                                0.14                                                                                                                                        0.17                                                      
LDL receptor related protein 12ENSG00000147650LRP12chr8:104489231-104589024:-                                                                                                                                                                                                  0.13                                                                0.42      
zinc finger DHHC-type palmitoyltransferase 4ENSG00000136247ZDHHC4chr7:6577434-6589374:+                                                                                                                                  0.11                            0.39                                            0.16        0.13        0.15                                              
tyrosine kinase non receptor 2ENSG00000061938TNK2chr3:195863364-195911945:-          0.19                                        0.35                                                                                                                                                    0.14                                                                  
transferrin receptorENSG00000072274TFRCchr3:196027183-196082189:-          0.19                                        0.35                                                                                                                                                    0.14                                                                  
ryanodine receptor 1ENSG00000196218RYR1chr19:38433699-38587564:+                                                                                                                                          0.54                                                                                                                              
discs large MAGUK scaffold protein 5ENSG00000151208DLG5chr10:77790791-77926526:-                                                                                                                                                          0.39                                0.15                                                                              
carbonic anhydrase 14ENSG00000118298CA14chr1:150257159-150265078:+                                                                                                                                                                          0.11                                0.21        0.22                                                      
RAB8A, member RAS oncogene familyENSG00000167461RAB8Achr19:16111629-16134234:+  0.29                                                                                                                                                                                                                                                0.24                      
solute carrier family 15 member 1ENSG00000088386SLC15A1chr13:98683801-98752654:-                  0.14                                                                                                        0.28        0.11                                                                                                                                      
BLK proto-oncogene, Src family tyrosine kinaseENSG00000136573BLKchr8:11494001-11564604:+                                                          0.53                                                                                                                                                                                                              

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