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 
transmembrane protein 255BENSG00000184497TMEM255Bchr13:113759240-113816995:+                                                                                                                                  0.11        0.22                                                                                                                              
G protein regulated inducer of neurite outgrowth 1ENSG00000169258GPRIN1chr5:176595802-176610133:-              0.11                                                                            0.33                                                                                                                                                                              
tetraspanin 17ENSG00000048140TSPAN17chr5:176647387-176659054:+              0.11                                                                            0.33                                                                                                                                                                              
unc-5 netrin receptor AENSG00000113763UNC5Achr5:176810477-176880895:+                                                                                          0.33                                                                                                                                                                              
cadherin related family member 2ENSG00000074276CDHR2chr5:176542511-176595974:+                                                                                          0.33                                                                                                                                                                              
histamine receptor H2ENSG00000113749HRH2chr5:175658030-175686242:+              0.11                                                                            0.33                                                                                                                                                                              
solute carrier family 52 member 3ENSG00000101276SLC52A3chr20:760080-776015:-                                                                                                                                                          0.33                                                                                                              
solute carrier family 19 member 2ENSG00000117479SLC19A2chr1:169463909-169486003:-                                                          0.22                                                                                                                                                                0.1                                              
solute carrier family 12 member 4ENSG00000124067SLC12A4chr16:67943474-67969601:-          0.17                                                                                                                                                    0.33                                                            0.15                                    0.14          
KIAA1549 likeENSG00000110427KIAA1549Lchr11:33542072-33674102:+          0.14        0.18                                                                                                                                                                                                                                                      
solute carrier family 29 member 4ENSG00000164638SLC29A4chr7:5274369-5306870:+                                                                                                                                                              0.41                                            0.16        0.16                                                      
adrenoceptor alpha 1BENSG00000170214ADRA1Bchr5:159916783-159972544:+                                                                                          0.32                                                                                                                    0.12                                                          
protein tyrosine phosphatase non-receptor type 4ENSG00000088179PTPN4chr2:119759631-119983818:+                                                          0.31                                                                                                                                                                                                              
ATP binding cassette subfamily C member 10ENSG00000124574ABCC10chr6:43427366-43450430:+                                          0.1                                                                                                                                                0.21                                                                              
Yip1 domain family member 3ENSG00000137207YIPF3chr6:43511827-43516990:-                                          0.1                                                                                                                                                0.21                                                                              
hydroxysteroid 17-beta dehydrogenase 7ENSG00000132196HSD17B7chr1:162790702-162812817:+                                                          0.21                                                                                                                                                                0.1                                              
hepatitis A virus cellular receptor 2ENSG00000135077HAVCR2chr5:157085832-157142869:-                                                                                          0.31                                                                                                                                                                              
hepatitis A virus cellular receptor 1ENSG00000113249HAVCR1chr5:157029413-157059119:-                                                                                          0.31                                                                                                                                                                              
solute carrier family 26 member 2ENSG00000155850SLC26A2chr5:149960737-149993455:+                                                                                          0.31                                                                                                                    0.14                                                          
solute carrier family 36 member 1ENSG00000123643SLC36A1chr5:151437046-151492381:+                                                                                          0.31                                                                                                                    0.14                                                          

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