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 
Bardet-Biedl syndrome 2ENSG00000125124BBS2chr16:56466836-56520283:-                                                                                                                                                                                                                          1                                    1          
C-X3-C motif chemokine ligand 1ENSG00000006210CX3CL1chr16:57372458-57385048:+                                                                                                                                                                                                                          1                                              
phosphatidylinositol glycan anchor biosynthesis class NENSG00000197563PIGNchr18:62043567-62187118:-                                              1    1            1                                                                                                                        1        1                                                                          
cholinergic receptor muscarinic 3ENSG00000133019CHRM3chr1:239386565-239915452:+                                                                                                                                                                                                                                                  1                      
RP2 activator of ARL3 GTPaseENSG00000102218RP2chrX:46836940-46882358:+                                                                                                                                  1                                                                                                                                      
smoothened, frizzled class receptorENSG00000128602SMOchr7:129188872-129213545:+                                                                                                                  1                                                                                                                                            1          
tetraspanin 33ENSG00000158457TSPAN33chr7:129144892-129169697:+                                                                                                                  1                                                                                                                                                      
catenin delta 1ENSG00000198561CTNND1chr11:57753243-57819546:+                                                          1                                                                                                                                                                                                    1          
syntaxin 4ENSG00000103496STX4chr16:31032889-31042975:+                                                                                                                                  1                                                                                                                                      
erythroblast membrane associated protein (Scianna blood group)ENSG00000164010ERMAPchr1:42817124-42844989:+                                                                                                                                  1                                                                                                                                      
adiponectin receptor 1ENSG00000159346ADIPOR1chr1:202940823-202958572:-                                                                                                                                                                                          1                                                                              
tetraspanin 13ENSG00000106537TSPAN13chr7:16753535-16784536:+                                                                                                                                  1                                                                                                                                      
solute carrier organic anion transporter family member 4A1ENSG00000101187SLCO4A1chr20:62642445-62685785:+                                                                                                                                                                                          1                                                                              
chromosome 1 open reading frame 210ENSG00000253313C1orf210chr1:43281883-43285617:-                                                                                                                                  1                                                                                                                                      
transmembrane protein 63AENSG00000196187TMEM63Achr1:225845536-225882369:-                                                                                                                                                                                                      1                                            1                      
jagged canonical Notch ligand 1ENSG00000101384JAG1chr20:10637684-10674107:-                                                                          1                                                                                                                                                                                              
EPH receptor A1ENSG00000146904EPHA1chr7:143390289-143408892:-                                                                                                                  1                                                                                                                                                      
GRIP and coiled-coil domain containing 1ENSG00000179562GCC1chr7:127580618-127593611:-                                                      1                                                            1                                                                                                                                            1          
dipeptidyl peptidase like 6ENSG00000130226DPP6chr7:153887097-154894285:+                                                                                                                  1                                                                                                                                                      
rhomboid like 2ENSG00000158315RHBDL2chr1:38885807-38941799:-                                                                                                                                  1                                                                                                                                      

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