Table 4.
Tabular summary of SVZ-dependent expression of genes
| 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 | ||||
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)