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 
G protein-coupled receptor 162ENSG00000250510GPR162chr12:6821545-6829972:+                                                                                                                                                                                                                          0.6                                              
pyrimidinergic receptor P2Y6ENSG00000171631P2RY6chr11:73264505-73298617:+                                                          0.6                                                                                                                                                                                                              
tweety family member 2ENSG00000141540TTYH2chr17:74213514-74262020:+                                                                                                                                                                                                  0.22        0.23                                                        0.14      
RELT TNF receptorENSG00000054967RELTchr11:73376264-73397474:+                                                          0.59                                                                                                                                                                                                              
TNF receptor superfamily member 1AENSG00000067182TNFRSF1Achr12:6328757-6342114:-                                                                                                                                                                                                                          0.58                                              
CD9 moleculeENSG00000010278CD9chr12:6199715-6238271:+                                                                                                                                                                                                                          0.58                                              
sodium channel epithelial 1 subunit alphaENSG00000111319SCNN1Achr12:6346843-6377730:-                                                                                                                                                                                                                          0.58                                              
lymphotoxin beta receptorENSG00000111321LTBRchr12:6375045-6391571:+                                                                                                                                                                                                                          0.58                                              
Rac family small GTPase 1ENSG00000136238RAC1chr7:6374523-6403977:+                                                                                                                                  0.11                            0.39                                            0.16        0.14        0.18                                              
diacylglycerol lipase betaENSG00000164535DAGLBchr7:6409126-6484190:-                                                                                                                                  0.11                            0.39                                            0.16        0.14        0.18                                              
phosphatidylinositol 4-kinase alphaENSG00000241973PI4KAchr22:20707691-20859417:-                                                                                                                                          0.29                                                                                0.29                                              
synaptosome associated protein 29ENSG00000099940SNAP29chr22:20858983-20891218:+                                                                                                                                          0.29                                                                                0.29                                              
limb development membrane protein 1ENSG00000105983LMBR1chr7:156668946-156893230:-      0.11                                                                                                                                        0.1            0.58                                                                                                    0.23          
hyaluronan synthase 2ENSG00000170961HAS2chr8:121612116-121641390:-                                                                                                                  0.2                                                                                0.19        0.19                                                              
potassium voltage-gated channel subfamily A member 5ENSG00000130037KCNA5chr12:5043989-5046788:+                                                                                                                                                                                                                          0.57                                              
syndecan 2ENSG00000169439SDC2chr8:96493351-96611780:+                                                                                                                                                                                                  0.18                                                                0.39      
transmembrane 7 superfamily member 3ENSG00000064115TM7SF3chr12:26973195-27014434:-                                                                                                                                                                                                                          0.57                                              
solute carrier family 2 member 3ENSG00000059804SLC2A3chr12:7919230-7936275:-                                                                                                                                                                                                                          0.57                                              
mannose-6-phosphate receptor, cation dependentENSG00000003056M6PRchr12:8940363-8949955:-                                                                                                                                                                                                                          0.57                                              
anoctamin 6ENSG00000177119ANO6chr12:45215987-45440404:+                                                                                                                                                                                                                                                          0.57              

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