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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)
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BMC Medicine

ISSN: 1741-7015

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