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 
CD3d moleculeENSG00000167286CD3Dchr11:118338954-118342744:-                      1                                                                                                                                                                                                                                                  
CD3g moleculeENSG00000160654CD3Gchr11:118344344-118355161:+                      1                                                                                                                                                                                                                                                  
MAM domain containing 4ENSG00000177943MAMDC4chr9:136850943-136860799:+                                                                                                                                                              1                                                                                                          
notch receptor 1ENSG00000148400NOTCH1chr9:136494444-136545862:-                                                                                                                                                              1                                                                                                          
CD3e moleculeENSG00000198851CD3Echr11:118304545-118316175:+                      1                                                                                                                                                                                                                                                  
quiescin sulfhydryl oxidase 2ENSG00000165661QSOX2chr9:136206333-136245841:-                                                                                                                                                              1                                                                                                          
TNF superfamily member 11ENSG00000120659TNFSF11chr13:42562736-42608013:+                              1                                                                                                                                                                                                                                          
sushi domain containing 4ENSG00000143502SUSD4chr1:223220819-223364202:-                                                                                                                                                                                                      1                                                                  
phospholipase A2 group IIAENSG00000188257PLA2G2Achr1:19975431-19980416:-                                                                                                                              1                                                                                                                                          
phospholipid phosphatase 1ENSG00000067113PPAP2Achr5:55424854-55535050:-                                                                                                                                                                                      1                                                                                  
phospholipase B domain containing 2ENSG00000151176PLBD2chr12:113358566-113391625:+                                      1                                                                                                                                                                                                                                  
cytoskeleton associated protein 4ENSG00000136026CKAP4chr12:106237877-106304279:-                                      1                                                                                                                                                                                                                                  
ectonucleoside triphosphate diphosphohydrolase 2ENSG00000054179ENTPD2chr9:137048098-137054045:-                                                                                                                                                              1                                                                                                          
leucine rich repeat containing 8 VRAC subunit BENSG00000197147LRRC8Bchr1:89524836-89597864:+                      1                                                                                                                                                                                        1                                                          
leucine rich repeat containing 8 VRAC subunit CENSG00000171488LRRC8Cchr1:89633072-89769903:+                      1                                                                                                                                                                                        1                                                          
neurexin 3ENSG00000021645NRXN3chr14:78242391-79868290:+                      1                                                                                                1                                                                                                                                                  
solute carrier family 30 member 2ENSG00000158014SLC30A2chr1:26037252-26046133:-                                                                                                                              1                                                                                                                                          
blood vessel epicardial substanceENSG00000112276BVESchr6:105096822-105137174:-              1                                                                                                                                                                                                1                                                          
ATPase phospholipid transporting 8B1ENSG00000081923ATP8B1chr18:57646426-57803101:-                                              1                                                                                        1                                                                                                                                  
ATPase H+ transporting V0 subunit a2ENSG00000185344ATP6V0A2chr12:123712318-123761755:+                                                                                                                                                                                                                                                              1          

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