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 
adiponectin receptor 2ENSG00000006831ADIPOR2chr12:1688574-1788678:+                  0.17                                                                                                                        0.22                0.46        0.13                                                        0.59                                              
fibroblast growth factor receptor 3ENSG00000068078FGFR3chr4:1793307-1808872:+          0.22                                                        0.11                                                                                                                                                                                        1.22              
ephrin A4ENSG00000243364EFNA4chr1:155063731-155069553:+  0.28                        0.2        0.53                        0.2                                                                                                                                0.11                0.2                                                              
carboxypeptidase MENSG00000135678CPMchr12:68842197-68971570:-          0.61                                                                                                                                                        0.11                                        0.32        0.45                                                      
RAB13, member RAS oncogene familyENSG00000143545RAB13chr1:153981617-153986358:-  0.21                        0.19                                0.22                                                                                                                                0.15        0.43        0.22                                                              
family with sequence similarity 189 member BENSG00000160767FAM189Bchr1:155247205-155255483:-  0.18                        0.19        0.65                        0.2                                                                                                                                                0.19                                                              
G protein-coupled receptor 160ENSG00000173890GPR160chr3:170037929-170085403:+                          0.75                                                                                                        0.23                                                0.11                                0.32                                                      
RAS p21 protein activator 3ENSG00000185989RASA3chr13:113977783-114132611:-                  0.17        0.23                                                0.15                                                0.29                0.19                                                        0.38                                                                      
ATPase phospholipid transporting 11AENSG00000068650ATP11Achr13:112690329-112887168:+                  0.15        0.23                                                0.16                                                0.29        0.12                                                                0.41                                                                      
zinc finger DHHC-type containing 11BENSG00000206077ZDHHC11Bchr5:710360-766952:-                                                                          0.16                                                                0.39                0.48                                                        0.18                                0.16                      
transmembrane protein 94ENSG00000177728KIAA0195chr17:75441159-75500090:+          0.21                0.24                                                                                                                0.25                                                        0.25        0.25                                                        0.14      
semaphorin 6CENSG00000143434SEMA6Cchr1:151131685-151146664:-                          0.22                                0.23                                                                                0.31                                                                0.22        0.22        0.11                                              
solute carrier family 26 member 11ENSG00000181045SLC26A11chr17:80219699-80253500:+          0.2                                                                                                                                0.22                0.42                                        0.19        0.24                                                              
ephrin A1ENSG00000169242EFNA1chr1:155127460-155134857:+                          0.2        0.53                        0.2                                                                                                                                0.11                0.2                                                              
EFR3 homolog AENSG00000132294EFR3Achr8:131904088-132013642:+                                                                                                                          0.37                                                                        0.15        0.21                                                        0.5      
G protein-coupled receptor 180ENSG00000152749GPR180chr13:94601903-94634645:+                  0.13        0.16                                                                                                0.24        0.11                                                                                                                        0.57              
GRB2 associated binding protein 2ENSG00000033327GAB2chr11:78215297-78418348:-                                                          0.23                                                                                                0.82                                                                                        0.14                      
nectin cell adhesion molecule 4ENSG00000143217PVRL4chr1:161070995-161089599:-          1.02                                                                                                                                                                                0.14                                                                              
phospholipase D1ENSG00000075651PLD1chr3:171600405-171810950:-          0.18                0.76                                                                                                                                                                                                0.2                                              
plexin A3ENSG00000130827PLXNA3chrX:154458281-154477779:+                          0.23                                                                                                        0.25                        0.45                                                        0.17                                                      

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