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 
C-type lectin domain containing 5AENSG00000258227CLEC5Achr7:141927357-141947007:-                                                                                                                  0.1                                                                                                                                                      
potassium voltage-gated channel subfamily H member 2ENSG00000055118KCNH2chr7:150944961-150978315:-                                                                                                                  0.1                                                                                                                                                      
solute carrier family 19 member 1ENSG00000173638SLC19A1chr21:45493572-45544411:-                                                                                                          0.1                                                    0.18                                                                                                          
proline rich 7, synapticENSG00000131188PRR7chr5:177446445-177456286:+                                                                                                                                                                                                          0.1                                                              
chondroitin polymerizing factor 2ENSG00000033100CHPF2chr7:151232489-151238827:+                                                                                                                  0.1                                                                                                                                            0.23          
serine protease 8ENSG00000052344PRSS8chr16:31131433-31135762:-                                                                                                                                  0.1                                                                                                                                      
myelin protein zeroENSG00000158887MPZchr1:161304735-161309972:-                                                                                                                                                                                                                          0.1                                              
solute carrier family 4 member 2ENSG00000164889SLC4A2chr7:151057210-151076527:+                                                                                                                  0.1                                                                                                                                            0.19          
cyclin dependent kinase 5ENSG00000164885CDK5chr7:151053812-151058530:-                                                                                                                  0.1                                                                                                                                            0.19          
thioredoxin related transmembrane protein 3ENSG00000166479TMX3chr18:68673688-68715298:-                                              0.15    0.1            0.18                                                                                                                        0.12        0.12                                                                          
solute carrier family 9 member A7ENSG00000065923SLC9A7chrX:46599252-46759172:-                                                                                                                                  0.1                                                                                                                                      
calsyntenin 1ENSG00000171603CLSTN1chr1:9729026-9824526:-                                      1.1                                                                                                        0.12        0.27                                        0.21                                0.11                                0.25          
chloride voltage-gated channel 6ENSG00000011021CLCN6chr1:11806096-11843144:+                              0.1        1.07                                                                                                        0.12        0.27                                        0.2                                                                0.25          
cell division cycle 42ENSG00000070831CDC42chr1:22052627-22092946:+                                      1.06                                                                                        0.22                0.11        0.23                                        0.21                                                                        0.12  
endothelin converting enzyme 1ENSG00000117298ECE1chr1:21217247-21345504:-                      0.19                1.11                                                                                        0.22                0.11                                                0.21                                                                          
glypican 1ENSG00000063660GPC1chr2:240435671-240468078:+      0.12        0.33        0.11        0.38                                                0.18                                        0.14                                        0.29                                                0.16                                                          
anoctamin 7ENSG00000146205ANO7chr2:241188509-241225377:+              0.33        0.11        0.38                                0.17                                                        0.15                        0.2                0.29                                                                                                          
XK related 8ENSG00000158156XKR8chr1:27959462-27968096:+                                      1.02                                                                                        0.21                        0.19                                        0.21                                                                          
lysophosphatidic acid receptor 6ENSG00000139679LPAR6chr13:48389567-48444704:-              0.34        0.2                                                        0.15                                                                0.18                                                        0.76                                                                  
G protein subunit beta 1ENSG00000078369GNB1chr1:1785285-1891117:-                              0.11                                                                                                0.31                0.11        0.27                                                0.28                        0.12                                0.27        0.14  

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