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 
par-6 family cell polarity regulator gammaENSG00000178184PARD6Gchr18:80157232-80247546:-              0.13                                                0.19                0.2                                                        0.1        0.14                0.44                        0.11        0.14        0.14                                                                  
alkaline phosphatase, biomineralization associatedENSG00000162551ALPLchr1:21509372-21578412:+                      0.19                1.06                                                                                        0.22                0.12                                                                                                                          
plexin B2ENSG00000196576PLXNB2chr22:50274979-50307627:-              0.12                                                        0.1                                                                0.12                        0.64                                        0.15                                                0.15        0.27          
lipase maturation factor 2ENSG00000100258LMF2chr22:50502949-50507691:-              0.12                                                        0.1                                                                0.12                        0.64                                        0.15                                                0.15        0.27          
G protein-coupled receptor 157ENSG00000180758GPR157chr1:9100305-9129170:-                              0.1        1.1                                                                                                        0.11                                                0.2                                                                          
solute carrier family 2 member 5ENSG00000142583SLC2A5chr1:9035107-9088478:-                                      1.1                                                                                        0.3                0.11                                                                                                                          
FAT atypical cadherin 1ENSG00000083857FAT1chr4:186587783-186726722:-              0.2                0.2                                0.17                0.23                                                        0.12        0.22                                                        0.33                                                                  
amyloid beta precursor like protein 2ENSG00000084234APLP2chr11:130069837-130144811:+              0.11                0.31                                                                                                                0.13                0.18                                        0.23        0.26                                                0.19          
interferon induced transmembrane protein 3ENSG00000142089IFITM3chr11:319669-327537:-                      0.14                                        0.15                                                                                0.16                0.5                                        0.26                                                        0.18          
TNF receptor superfamily member 1BENSG00000028137TNFRSF1Bchr1:12167003-12209228:+                                      1.07                                                                                                        0.11                                                0.2                                                                          
chromosome 1 open reading frame 159ENSG00000131591C1orf159chr1:1081818-1116361:-                              0.11                                                                                                0.31                0.11        0.27                                                0.28                        0.12                                        0.14  
G protein-coupled receptor 35ENSG00000178623GPR35chr2:240605431-240631259:+                      0.11        0.38                                0.17                0.19                                                                0.19                0.29                                                                                                          
TNF receptor superfamily member 10cENSG00000173535TNFRSF10Cchr8:23084355-23117437:+              0.15                                0.12        0.11                                                                        0.13                                                        0.24        0.18                                                        0.11        0.24          
solute carrier family 30 member 5ENSG00000145740SLC30A5chr5:69093646-69131069:+                                      0.13                        0.16                                                                                                0.72                        0.21                                                                                  
solute carrier family 45 member 1ENSG00000162426SLC45A1chr1:8317826-8344167:+                                      1.1                                                                                                        0.12                                                                                                                          
single Ig and TIR domain containingENSG00000185187SIGIRRchr11:405716-417455:-                      0.14                                        0.15                                                                                0.16                0.5                                        0.26                                                                  
STT3 oligosaccharyltransferase complex catalytic subunit AENSG00000134910STT3Achr11:125591712-125625215:+              0.11                0.32        0.19                                                                                                                        0.17                                        0.25                                                        0.17          
G protein-coupled receptor 153ENSG00000158292GPR153chr1:6247346-6260975:-                              0.1                                                                                                0.32                0.11        0.31                                        0.2                0.15                                                          
solute carrier family 9 member A1ENSG00000090020SLC9A1chr1:27098815-27166981:-                                              0.18                                                                                                0.11        0.19        0.47                                0.22                                                                          
TNF receptor superfamily member 10bENSG00000120889TNFRSF10Bchr8:23020133-23069179:-              0.15                                0.12                                                                                0.13                                                        0.24        0.18                                                        0.11        0.24          

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