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 family 7 member 6ENSG00000103064SLC7A6chr16:68264516-68301823:+          0.16                                                                                                                                                    0.32                                                                                                          
potassium voltage-gated channel modifier subfamily S member 3ENSG00000170745KCNS3chr2:17877847-18361616:+                                                                                                                                                                                                                          0.16                                              
heat shock protein family D (Hsp60) member 1ENSG00000144381HSPD1chr2:197486581-197516737:-                          0.16                                                                                                                                                                                                                                              
par-6 family cell polarity regulator alphaENSG00000102981PARD6Achr16:67660946-67662778:+          0.16                                                                                                                                                    0.31                                                                                                          
tetratricopeptide repeat domain 17ENSG00000052841TTC17chr11:43358932-43494933:+                                                          0.15                                                                                                                                                                                                              
neuropeptides B and W receptor 1ENSG00000183729NPBWR1chr8:52938431-52941117:+                                                                                                                                                                                                                          0.15                                              
G protein-coupled receptor 146ENSG00000164849GPR146chr7:1044576-1059261:+                                                                                                                                                              0.4                                            0.15                                                              
cyclin and CBS domain divalent metal cation transport mediator 4ENSG00000158158CNNM4chr2:96760902-96811891:+                                                                                                                                                                                                  0.15                                                                      
cyclin and CBS domain divalent metal cation transport mediator 3ENSG00000168763CNNM3chr2:96816245-96833911:+                                                                                                                                                                                                  0.15                                                                      
opioid related nociceptin receptor 1ENSG00000125510OPRL1chr20:64080173-64100643:+                                                                                                                                                                                                          0.15                                                              
EH domain containing 1ENSG00000110047EHD1chr11:64851642-64888296:-                                                          0.15                                                                                                                                                                                                              
adhesion G protein-coupled receptor G2ENSG00000173698ADGRG2chrX:18989309-19122637:-                                                                                                                                                                                                  0.15                                                                      
filamin AENSG00000196924FLNAchrX:154348524-154374638:-                                                                          0.15                                                                                                                                                                                              
solute carrier family 13 member 3ENSG00000158296SLC13A3chr20:46557823-46684467:-                                                                                                                                                                                          0.15                                                                              
plexin B3ENSG00000198753PLXNB3chrX:153764196-153779346:+                                                                          0.14                                                                                                                                                                                              
EH domain containing 3ENSG00000013016EHD3chr2:31234337-31269447:+                                                                                                                                                                                                                          0.14                                              
CASP8 and FADD like apoptosis regulatorENSG00000003402CFLARchr2:201116104-201176687:+                          0.14                                                                                                                                                                                                                                              
family with sequence similarity 126 member BENSG00000155744FAM126Bchr2:200973718-201071671:-                          0.14                                                                                                                                                                                                                                              
EH domain containing 2ENSG00000024422EHD2chr19:47713343-47743134:+  0.14                                                                                                                                            0.11                0.33                                                                                                          
stomatin like 2ENSG00000165283STOML2chr9:35099776-35103195:-                                                                                                                                                                                                                  0.14                                                      

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