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 
RAS guanyl releasing protein 1ENSG00000172575RASGRP1chr15:38488103-38565575:-                                                                      0.13                                                                0.11                0.37                                                        0.17                                                          
solute carrier family 26 member 6ENSG00000225697SLC26A6chr3:48625723-48635493:-                      0.16                                0.11                                        0.18                                                                0.2                                        0.13                                                                  
CD164 moleculeENSG00000135535CD164chr6:109366514-109382559:-              0.13                        0.15                0.25                                                                                                0.14                                                        0.12                                                          
insulin like growth factor 2 receptorENSG00000197081IGF2Rchr6:159969099-160113507:+                                                                                                                                                      0.18        0.44                                                0.15                                                          
pannexin 2ENSG00000073150PANX2chr22:50170731-50180294:+                                                                                                                                      0.12                        0.64                                                                                                          
ezrinENSG00000092820EZRchr6:158765741-158819412:-                                      0.18                                                                                                                        0.44                                                0.15                                                          
atypical chemokine receptor 3ENSG00000144476ACKR3chr2:236567787-236582358:+              0.32                                                                0.19                                                                                0.26                                                                                                          
TNF receptor superfamily member 10dENSG00000173530TNFRSF10Dchr8:23135588-23164030:-                                              0.12                                                                                0.12                                                        0.24        0.17                                                        0.11                  
protein tyrosine phosphatase receptor type DENSG00000153707PTPRDchr9:8314246-10612723:-                                                                              0.27                                        0.13                0.24                                0.12                                                                                                  
signal peptide peptidase like 2BENSG00000005206SPPL2Bchr19:2328615-2354806:+                                                                                                                                                                                                                                                              0.75          
shadow of prion proteinENSG00000203772SPRNchr10:133420666-133424572:-              0.1        0.13                                                                                                0.14                                                                                0.21                        0.17                                          
occludinENSG00000197822OCLNchr5:69492292-69558104:+                                                                                                                                                              0.74                                                                                                          
cadherin EGF LAG seven-pass G-type receptor 3ENSG00000008300CELSR3chr3:48636469-48662915:-                      0.16                0.24                                                                                                                        0.2                                        0.13                                                                  
TNF receptor superfamily member 25ENSG00000215788TNFRSF25chr1:6461151-6466195:-                              0.1                                                                                                                0.11        0.31                                        0.2                                                                          
G protein subunit alpha i2ENSG00000114353GNAI2chr3:50226292-50259355:+                      0.17                0.2                                                                                                                        0.18                                        0.17                                                                  
dystroglycan 1ENSG00000173402DAG1chr3:49468703-49535618:+                      0.17                                                                        0.18                                                                0.19                                        0.16                                                                  
RALBP1 associated Eps domain containing 1ENSG00000135597REPS1chr6:138903493-138988261:-                                      0.1                0.19                0.12                                                                                0.17                                                        0.13                                                          
cyclin and CBS domain divalent metal cation transport mediator 2ENSG00000148842CNNM2chr10:102918293-103090221:+              0.1                                0.11                                                                                                        0.18        0.31                                                                                                          
coagulation factor II thrombin receptorENSG00000181104F2Rchr5:76716043-76735781:+                                                                                                                                                              0.7                                                                                                          
serine incorporator 5ENSG00000164300SERINC5chr5:80111651-80256079:-                                                                                                                                                              0.67                                                                                                          

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