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 
immunoglobulin superfamily member 9BENSG00000080854IGSF9Bchr11:133908564-133956985:-                                                                                                                                                              0.21                                                                                                          
N-acetylated alpha-linked acidic dipeptidase like 2ENSG00000177694NAALADL2chr3:174438573-175810552:+                                                                                                                                                                                                                      0.21                                                  
interferon lambda receptor 1ENSG00000185436IFNLR1chr1:24154157-24187959:-                                                                                                                                                                                              0.21                                                                          
interleukin 22 receptor subunit alpha 1ENSG00000142677IL22RA1chr1:24119771-24143121:-                                                                                                                                                                                              0.2                                                                          
olfactomedin 4ENSG00000102837OLFM4chr13:53028759-53052057:+                              0.2                                                                                                                                                                                                                                          
syndecan 3ENSG00000162512SDC3chr1:30869467-30908761:-                                                                                                                                                                                              0.2                                                                          
cadherin related family member 4ENSG00000187492CDHR4chr3:49790732-49799835:-                                                                                                                                                              0.2                                                                                                          
ATPase H+ transporting V0 subunit a1ENSG00000033627ATP6V0A1chr17:42458844-42522611:+                                                                                                                                                                                                                                                              0.2          
RAB5C, member RAS oncogene familyENSG00000108774RAB5Cchr17:42124976-42155044:-                                                                                                                                                                                                                                                              0.2          
transmembrane protein 231ENSG00000205084TMEM231chr16:75536744-75556286:-                                                                                                                                                                                                                                                              0.19          
leukocyte receptor tyrosine kinaseENSG00000062524LTKchr15:41503638-41513887:-                                                                                                                                                                                                              0.19                                                          
serine incorporator 2ENSG00000168528SERINC2chr1:31409565-31434680:+                                                                                                                              0.19                                                                                                                                          
solute carrier family 1 member 1ENSG00000106688SLC1A1chr9:4490444-4587469:+                                                                                                                                                              0.19                                                                                                          
solute carrier family 2 member 8ENSG00000136856SLC2A8chr9:127397138-127408424:+                                                                                                                                                                                                                                                              0.19          
leucine rich repeat containing 37AENSG00000176681LRRC37Achr17:46292733-46337794:+                                                                                                                                                                                                                                                              0.19          
leucine rich repeat containing 37 member A2ENSG00000238083LRRC37A2chr17:46511511-46555650:+                                                                                                                                                                                                                                                              0.19          
C-X-C motif chemokine receptor 2ENSG00000180871CXCR2chr2:218125289-218137253:+                                                                                                                                              0.19                                                                                                                          
scavenger receptor cysteine rich family member with 5 domainsENSG00000179954SSC5Dchr19:55488404-55519098:+                                                                                                                      0.19                                                                                                                                                  
5-hydroxytryptamine receptor 2BENSG00000135914HTR2Bchr2:231108230-231125118:-                                                                                                                                              0.19                                                                                                                          
histamine receptor H1ENSG00000196639HRH1chr3:11137093-11263557:+                                      0.18                                                                                                                                                                                                                                  

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