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 
ectonucleotide pyrophosphatase/phosphodiesterase 1ENSG00000197594ENPP1chr6:131808016-131895155:+                                      0.1                                0.1                                                                                0.13                                                        0.12                                                          
myoferlinENSG00000138119MYOFchr10:93306429-93482317:-                                                                                                                                                      0.14        0.32                                                                                                          
gap junction protein beta 2ENSG00000165474GJB2chr13:20187470-20192898:-                                                                              0.18                                                                0.14        0.14                                                                                                                  
nectin cell adhesion molecule 1ENSG00000110400PVRL1chr11:119623408-119729084:-                                                                                                                                                                                                      0.25                                                        0.19          
protein kinase N2ENSG00000065243PKN2chr1:88684222-88836255:+                                                                                                                                                      0.33                                                        0.11                                                          
tetraspanin 4ENSG00000214063TSPAN4chr11:842808-867116:+                                                                                                                      0.11                        0.17                                                                                                                0.15          
signal peptide peptidase like 3ENSG00000157837SPPL3chr12:120762510-120904371:-                                      0.17                                                                                                                                                                                                                        0.26          
ADAM metallopeptidase domain 8ENSG00000151651ADAM8chr10:133262403-133276868:-                                                                                                                      0.14                                                                                        0.11                0.17                                          
semaphorin 4GENSG00000095539SEMA4Gchr10:100969518-100985871:+              0.1                                                                                                                                                0.33                                                                                                          
KN motif and ankyrin repeat domains 1ENSG00000107104KANK1chr9:470291-746106:+                                                                                                                                                              0.21                                        0.22                                                                  
interferon induced protein with tetratricopeptide repeats 5ENSG00000152778IFIT5chr10:89414586-89421001:+                                                              0.13                                                                                                0.3                                                                                                          
erythrocyte membrane protein band 4.1ENSG00000159023EPB41chr1:28887091-29120046:+                                                                                                                              0.21                                                                0.21                                                                          
RAB11 family interacting protein 2ENSG00000107560RAB11FIP2chr10:118004916-118046603:-                                                                                                                      0.12        0.11                        0.19                                                                                                                  
major facilitator superfamily domain containing 4BENSG00000173214KIAA1919chr6:111259348-111271167:+              0.13                        0.15                                                                                                                                                                        0.14                                                          
sidekick cell adhesion molecule 1ENSG00000146555SDK1chr7:3301448-4269000:+                                                                                                                                                              0.42                                                                                                          
phospholipid phosphatase 2ENSG00000141934PPAP2Cchr19:281040-291504:-              0.15                                                                                                                        0.11        0.16                                                                                                                          
neuralized E3 ubiquitin protein ligase 1ENSG00000107954NEURL1chr10:103493979-103592552:+                                              0.1                                                                                                                0.31                                                                                                          
toll interacting proteinENSG00000078902TOLLIPchr11:1274371-1309654:-                                                              0.14                                                        0.11                        0.16                                                                                                                          
collagen type VI alpha 3 chainENSG00000163359COL6A3chr2:237324003-237414375:-              0.31        0.11                                                                                                                                                                                                                                                  
lymphocyte cytosolic protein 1ENSG00000136167LCP1chr13:46125920-46211871:-                                                                                                                                                                                      0.41                                                                                  

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