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 
leucine rich repeat and fibronectin type III domain containing 1ENSG00000128011LRFN1chr19:39306568-39315336:-                                                                                                                                                          0.78                                                                                                              
semaphorin 4BENSG00000185033SEMA4Bchr15:90160604-90229679:+                          0.19                                0.28                                                                                                                                0.11                0.19                                                              
LDL receptor related protein 5ENSG00000162337LRP5chr11:68312609-68449275:+                                                          0.77                                                                                                                                                                                                              
prolyl 4-hydroxylase subunit betaENSG00000185624P4HBchr17:81843159-81860694:-          0.22                                                                                                                                                                                        0.17        0.24                                                        0.14      
chromosome 11 open reading frame 24ENSG00000171067C11orf24chr11:68261335-68272001:-                                                          0.76                                                                                                                                                                                                    0.1          
hyperpolarization activated cyclic nucleotide gated potassium channel 3ENSG00000143630HCN3chr1:155277583-155289848:+  0.18                        0.19                                0.2                                                                                                                                                0.19                                                              
delta like canonical Notch ligand 3ENSG00000090932DLL3chr19:39498895-39508481:+                                                                                                                                                          0.76                                                                                                    0.11          
IQ motif containing GTPase activating protein 1ENSG00000140575IQGAP1chr15:90388218-90502243:+                          0.18                                0.27                                                                                                                                0.1                0.2                                                              
calcium and integrin binding 1ENSG00000185043CIB1chr15:90229975-90234047:-                          0.17                                0.28                                                                                                                                0.1                0.19                                                              
activity regulated cytoskeleton associated proteinENSG00000198576ARCchr8:142611044-142614472:-                                                                                                                                                                                                          0.24                                                        0.5      
adhesion G protein-coupled receptor B1ENSG00000181790ADGRB1chr8:142449430-142545009:+                                                                                                                                                                                                          0.23                                                        0.5      
transmembrane protein 123ENSG00000152558TMEM123chr11:102396332-102470384:-          0.29                                                0.14                                                                                                                                        0.3                                                                      
calcium voltage-gated channel subunit alpha1 CENSG00000151067CACNA1Cchr12:1970786-2697950:+                                          0.16                                                                                                                                                                                0.57                                              
steroid 5 alpha-reductase 3ENSG00000128039SRD5A3chr4:55346109-55373096:+                          0.13                                                                                                                                                                        0.22                        0.37                                              
solute carrier family 45 member 4ENSG00000022567SLC45A4chr8:141207166-141308305:-                                                                                                                                                                                                          0.22                                                        0.5      
clathrin heavy chainENSG00000141367CLTCchr17:59619689-59696956:+          0.23                                                                                                                                                            0.13                    0.11        0.17        0.21                                                              
FCH and double SH3 domains 2ENSG00000137478FCHSD2chr11:72836745-73142261:-                                                          0.72                                                                                                                                                                                                    0.1          
jagged canonical Notch ligand 2ENSG00000184916JAG2chr14:105140981-105168824:-                                                                                                                                          0.2                0.38                                                                                        0.12                      
furin, paired basic amino acid cleaving enzymeENSG00000140564FURINchr15:90868592-90883458:+                          0.18                                0.22                                                                                                                                0.1                0.2                                                              
SLC9A3 regulator 1ENSG00000109062SLC9A3R1chr17:74748652-74769353:+          0.21                                                                                                                                0.23                                                                0.24                                                              

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