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Table 4 Tabular summary of SVZ-dependent expression of genes

From: Spatial transcriptome analysis reveals Notch pathway-associated prognostic markers in IDH1 wild-type glioblastoma involving the subventricular zone

Gene Microarray cohort (n = 36) Selected for validation Validation cohort (n = 142)
SVZ+ vs. SVZ– II vs. III SVZ+ vs. SVZ– II vs. III Expression in SVZ+/II
p value FC qPCR p value FC qPCR p value p value  
PIR 0.0188 0.4770 0.0082 0.0047 0.7338 0.0225 0.1597 0.05 Low
HES4 0.3680 −0.0135 0.0015 0.0440 −0.5945 0.5584 0.0102 0.0007 High
DLL3 0.5645 −0.7725 0.1407 0.0654 −1.5897 0.0295 0.9516 0.0857 High (trend)
NTRK2 0.0511 0.2464 0.5821 0.0304 0.5708 0.0559 0.7883 0.0558 High (trend)
IGFBP5 0.0134 0.4772 0.0066 0.0234 1.2149 0.1179 0.8477 0.9498
BAI3 0.3676 −0.0817 0.1829 0.0290 −0.5699 0.0714 0.2911 0.8653  
EMILIN3 0.0810 0.3924 0.3921 0.0290 0.7203 0.0312 0.6789 0.5567  
FERMT2 0.0109 −0.1693 0.0058 0.0088 −0.8139 0.0017 0.7765 0.1156  
CDH4 0.0197 −0.3874 0.0168 0.0929 −0.7704 0.0120 0.2006 0.7516  
UCHL1 0.0168 0.3306 0.1369 0.2702 0.1823 0.7063     
HIF1A 0.0052 −0.1433 0.0215 0.1274 −0.1174 0.5345 0.6371 0.7699  
TGFB3 0.0021 −0.5547 0.2056 0.0570 −0.6072 0.3000     
RBP1 0.0017 0.6986 0.0186 0.0035 1.2351 0.0312 0.9776 0.6936  
SYTL4 0.1318 0.0785 0.2347 0.0035 1.0968 0.0075 0.3189 0.4702  
THBS4 0.0155 0.1638 0.1810 0.0096 0.8009 0.0072 0.4495 0.9817  
NODAL 0.0043 −0.4242 0.3117 0.0225 −0.4279 0.2625     
FZD6 0.1895 0.1517 0.4073 0.0014 0.6362 0.0730     
VAV3 0.0873 0.1032 0.5665 0.0235 0.8138 0.4895     
ENPP5 0.3551 0.2665 0.0397 0.0218 0.6382 0.0116     
TIMP4 0.4696 0.1804 0.1286 0.0417 0.5615 0.1179     
NDN 0.0107 0.8016 0.2038 0.2543 1.3415 0.9458     
NFKBIA 0.0149 −0.1440 0.3924 0.0144 −0.3358 0.2515     
IRF9 0.0750 −0.0766 0.2604 0.0157 −0.5397 0.2630     
BATF3 0.1257 −0.1263 0.0414 0.0087 −0.6015 0.6570     
ANGPTL2 0.2385 −0.1070 0.5178 0.0187 −0.6711 0.7632     
PDGFRA 0.9394 −0.0442 0.2959 0.0453 −1.1161 0.0714     
  1. First, mRNA microarray data were compared between SVZ+ and SVZ– GBM and group II and group III GBM, respectively (in bold: p < 0.01 (two-sided t test), log2 fold change (FC) >0.5/<–0.5) with technical validation of differential gene expression by qPCR (in bold: p < 0.05 (two-sided Mann-Whitney test)) (microarray cohort). Based on the prespecified significance levels, 13 candidate genes (indicated by check marks) were chosen for validation of differential gene expression by qPCR (in bold: p < 0.05 (two-sided Mann-Whitney test)) in a confirmatory patient cohort (validation cohort)