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 
Rho related BTB domain containing 2ENSG00000008853RHOBTB2chr8:22987417-23020199:+              0.15                                0.12                                                                                0.13                                                        0.24        0.17                                                        0.11        0.24          
TYRO3 protein tyrosine kinaseENSG00000092445TYRO3chr15:41557675-41583586:+                              0.11                                        0.12                                                                                0.36        0.39                                                0.19                                                          
TNF receptor superfamily member 10aENSG00000104689TNFRSF10Achr8:23190452-23225126:-              0.15                                0.12                                                                                0.12                                                        0.24        0.18                                                        0.11        0.24          
solute carrier family 39 member 14ENSG00000104635SLC39A14chr8:22367249-22434129:+              0.14                                0.12                                                                                0.13                                                        0.23        0.17                                                        0.11        0.24          
ATPase Na+/K+ transporting subunit beta 2ENSG00000129244ATP1B2chr17:7646627-7657768:+                                                                                                                              0.16                                                        0.27                0.69                                                                  
ras homolog family member AENSG00000067560RHOAchr3:49359145-49412998:-                      0.17                0.24                0.16                                        0.18                                                                0.19                                        0.16                                                                  
transmembrane protein 259ENSG00000182087TMEM259chr19:1009648-1021179:-              0.14                                                0.18                                                                                                                                                                                                0.78          
enolase 1ENSG00000074800ENO1chr1:8861002-8879249:-                              0.1                                                                                                0.29                0.11        0.27                                        0.2                                0.11                                          
ADP ribosylation factor like GTPase 4CENSG00000188042ARL4Cchr2:234493041-234497053:-              0.31                0.38                                                0.18                                                                0.2                                                                                                                          
chromosome 6 open reading frame 120ENSG00000185127C6orf120chr6:169702190-169704856:+                                      0.24                                                                                        0.19                                0.46                                                0.17                                                          
radixinENSG00000137710RDXchr11:110174880-110296722:-              0.11        0.22                                                        0.17                                                                        0.12                                                0.24                                                        0.19          
SID1 transmembrane family member 2ENSG00000149577SIDT2chr11:117178733-117197445:+              0.11        0.24        0.29                                                                                                                                                                        0.23                                                        0.18          
insulin receptor substrate 1ENSG00000169047IRS1chr2:226731317-226799759:-              0.31                0.37                                                0.18                                                                0.19                                                                                                                          
toll like receptor 3ENSG00000164342TLR3chr4:186069152-186088069:+              0.19        0.12                                        0.12                0.16                                                        0.12                                                                0.33                                                                  
integral membrane protein 2CENSG00000135916ITM2Cchr2:230864639-230879248:+              0.32                0.37                                0.15                                                                                0.19                                                                                                                          
ring finger protein 26ENSG00000173456RNF26chr11:119334527-119337313:+              0.11                0.31        0.17                                                                                                                                                                0.24                                                        0.17          
suppression of tumorigenicity 14ENSG00000149418ST14chr11:130159562-130210376:+              0.11                0.31                                                                                                                0.13                0.19                                                0.26                                                          
angio associated migratory cell proteinENSG00000127837AAMPchr2:218264123-218270257:-                              0.34                                0.13                0.18                                                                0.19        0.12                                                                                                                  
MARVEL domain containing 2ENSG00000152939MARVELD2chr5:69415112-69444330:+                                                                                                                                                              0.73                        0.21                                                                                  
solute carrier family 39 member 9ENSG00000029364SLC39A9chr14:69398015-69462388:+                      0.1                0.33                                                                                0.11                                        0.26                                        0.14                                                                  

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