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 
proton activated chloride channel 1ENSG00000065600TMEM206chr1:212363931-212414901:-                                                                                                                                                              0.17                                                                                                          
calcium voltage-gated channel subunit alpha1 DENSG00000157388CACNA1Dchr3:53494656-53813733:+                      0.16                                                                                                                                                                                                                                                  
lymphocyte specific protein 1ENSG00000130592LSP1chr11:1852970-1892267:+                                                                                                                                              0.16                                                                                                                          
solute carrier family 22 member 18ENSG00000110628SLC22A18chr11:2899721-2925246:+                                                                                                                                              0.16                                                                                                                          
CD68 moleculeENSG00000129226CD68chr17:7579467-7582113:+                                                                                                                              0.16                                                                                                                                          
cyclase associated actin cytoskeleton regulatory protein 2ENSG00000112186CAP2chr6:17393216-17557792:+                                                              0.16                                                                                                                                                                                                          
family with sequence similarity 234 member BENSG00000084444KIAA1467chr12:13044284-13142521:+                                                                                                                                                                                                      0.16                                                                  
TNF superfamily member 12ENSG00000239697TNFSF12chr17:7548891-7557890:+                                                                                                                              0.16                                                                                                                                          
potassium two pore domain channel subfamily K member 2ENSG00000082482KCNK2chr1:215005775-215237093:+                                                                                                                                                              0.16                                                                                                          
ATP binding cassette subfamily B member 9ENSG00000150967ABCB9chr12:122920951-122981649:-                                                                                                                                                                                                                                                              0.16          
golgi membrane protein 1ENSG00000135052GOLM1chr9:86026146-86100173:-                                                                                                                                                                                                                                                              0.15          
G protein subunit alpha qENSG00000156052GNAQchr9:77716087-78031458:-                                                                                                                                                                                                                                                              0.15          
neuroligin 2ENSG00000169992NLGN2chr17:7404874-7419860:+                                                                                                                              0.15                                                                                                                                          
cholinergic receptor nicotinic beta 1 subunitENSG00000170175CHRNB1chr17:7445061-7457707:+                                                                                                                              0.15                                                                                                                                          
phospholipid scramblase 3ENSG00000187838TMEM256-PLSCR3chr17:7389727-7394843:-                                                                                                                              0.15                                                                                                                                          
gap junction protein alpha 1ENSG00000152661GJA1chr6:121435692-121449727:+                                                                                                                                                      0.15                                                                                                                  
solute carrier family 31 member 1ENSG00000136868SLC31A1chr9:113221562-113264492:+                                                                                                                                                                                                                                                              0.15          
ATP binding cassette subfamily A member 7ENSG00000064687ABCA7chr19:1040101-1065572:+              0.15                                                                                                                                                                                                                                                          
LHFPL tetraspan subfamily member 2ENSG00000145685LHFPL2chr5:78485215-78770021:-                                                              0.15                                                                                                                                                                                                          
protocadherin 1ENSG00000156453PCDH1chr5:141853111-141879246:-                                                                                                                                                                                                              0.15                                                          

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