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 
adrenoceptor alpha 1AENSG00000120907ADRA1Achr8:26748150-26867273:-                                                                                                                              0.11                                                                                                                                          
protein O-mannosyltransferase 2ENSG00000009830POMT2chr14:77274956-77320884:-                                                                                                                      0.11                                                                                                                                                  
vascular cell adhesion molecule 1ENSG00000162692VCAM1chr1:100719742-100739045:+                      0.11                                                                                                                                                                                                                                                  
cadherin 13ENSG00000140945CDH13chr16:82626803-83800640:+                                                                              0.11                                                                                                                                                                                          
TNF receptor superfamily member 8ENSG00000120949TNFRSF8chr1:12063377-12144207:+                                                                                                                                              0.11                                                                                                                          
solute carrier family 7 member 5ENSG00000103257SLC7A5chr16:87830023-87869488:-                                                                                                                                      0.11                                                                                                                                  
cadherin EGF LAG seven-pass G-type receptor 1ENSG00000075275CELSR1chr22:46360834-46537170:-                                                                                                                                      0.11                                                                                                                                  
adhesion G protein-coupled receptor D1ENSG00000111452ADGRD1chr12:130953907-131141469:+                                                                                                                              0.11                                                                                                                                          
potassium two pore domain channel subfamily K member 10ENSG00000100433KCNK10chr14:88180103-88326907:-                                                                                                                      0.11                                                                                                                                                  
phospholipase D family member 3ENSG00000105223PLD3chr19:40348456-40380439:+                                                                                                                                                                                                                                                              0.11          
dystrophinENSG00000198947DMDchrX:31097677-33339441:-                                                                                                                                              0.11                                                                                                                          
periaxinENSG00000105227PRXchr19:40393768-40413366:-                                                                                                                                                                                                                                                              0.11          
solute carrier family 8 member A3ENSG00000100678SLC8A3chr14:70044217-70189070:-                                                                                                                      0.11                                                                                                                                                  
dipeptidase 1ENSG00000015413DPEP1chr16:89613308-89638456:+                                                                                                                                                                                                              0.11                                                          
protein tyrosine phosphatase receptor type N2ENSG00000155093PTPRN2chr7:157539056-158587788:-      0.11                                                                                                                                                                                                                                                                  
ATP binding cassette subfamily A member 4ENSG00000198691ABCA4chr1:93992835-94121132:-                      0.11                                                                                                                                                                                                                                                  
polycystin 2, transient receptor potential cation channelENSG00000118762PKD2chr4:88007668-88077777:+                                                                                                                              0.11                                                                                                                                          
ATP binding cassette subfamily G member 2 (Junior blood group)ENSG00000118777ABCG2chr4:88090264-88231322:-                                                                                                                              0.11                                                                                                                                          
heparan sulfate 2-O-sulfotransferase 1ENSG00000153936HS2ST1chr1:86914648-87109998:+                                                                                                                                                                                                              0.11                                                          
solute carrier family 44 member 3ENSG00000143036SLC44A3chr1:94820342-94895246:+                      0.11                                                                                                                                                                                                                                                  

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