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 
secretory carrier membrane protein 4ENSG00000227500SCAMP4chr19:1905214-1926013:+                                                              0.17                                                                                                                                                                                                0.77          
sorting nexin 9ENSG00000130340SNX9chr6:157700387-157945077:+                                      0.18                                                                                                                0.15        0.45                                                0.15                                                          
transmembrane protein 181ENSG00000146433TMEM181chr6:158536436-158635428:+                                      0.18                                                                                                                0.17        0.44                                                0.15                                                          
integral membrane protein 2BENSG00000136156ITM2Bchr13:48233158-48270357:+                              0.24                                                0.14                                                                        0.16                                0.39                                                                                  
CD58 moleculeENSG00000116815CD58chr1:116514535-116571039:-                                                      0.28        0.15                0.16                                                        0.14        0.19                                                                                                                          
EPS8 like 2ENSG00000177106EPS8L2chr11:694438-727727:+                                                              0.15                                                        0.11                        0.16                0.5                                                                                                          
InaF motif containing 2ENSG00000259330INAFM2chr15:40325216-40326715:+                                                                      0.12                                                                0.11                                                                        0.18                                                0.52          
endothelin converting enzyme like 1ENSG00000171551ECEL1chr2:232479827-232487828:-              0.33                0.39                                                                                                                0.2                                                                                                                          
transmembrane protein 171ENSG00000157111TMEM171chr5:73120292-73131817:+                                                              0.16                                                                                                0.71                                                                                                          
beta-secretase 1ENSG00000186318BACE1chr11:117285207-117316259:-              0.1        0.24        0.29                                                                                                                                                                        0.23                                                                  
HYLS1 centriolar and ciliogenesis associatedENSG00000198331HYLS1chr11:125883614-125900648:+              0.11                0.32                                                                                                                                0.17                                        0.26                                                                  
F2R like trypsin receptor 1ENSG00000164251F2RL1chr5:76818933-76835315:+                                                              0.15                                                                                                0.7                                                                                                          
TNF receptor superfamily member 14ENSG00000157873TNFRSF14chr1:2555639-2565382:+                                                                                                                              0.31                0.11        0.27                                                                                                                0.14  
sterol-C5-desaturaseENSG00000109929SC5Dchr11:121292453-121308694:+              0.11                0.31                                                                                                                                                                        0.24                                                        0.17          
secretory carrier membrane protein 1ENSG00000085365SCAMP1chr5:78360583-78479071:+                                                              0.15                                                                                                0.68                                                                                                          
osteoclastogenesis associated transmembrane protein 1ENSG00000081087OSTM1chr6:108041409-108165854:-              0.13                        0.15                0.26                                                                                                0.14                                                        0.13                                                          
anoctamin 9ENSG00000185101ANO9chr11:417933-442011:-                      0.14                                                                                                                        0.16                0.5                                                                                                          
plakophilin 3ENSG00000184363PKP3chr11:392614-404908:+                      0.14                                                                                                                        0.16                0.5                                                                                                          
transmembrane protein 25ENSG00000149582TMEM25chr11:118531041-118547280:+              0.11                0.3                                                                                                                                                                        0.23                                                        0.15          
ATPase cation transporting 13A2ENSG00000159363ATP13A2chr1:16985958-17011928:-                      0.21                                                                                                                        0.11        0.26                                        0.21                                                                          

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