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Table 3 Top five prognosis-related canonical pathways in Group 3

From: Subgroup-specific prognostic signaling and metabolic pathways in pediatric medulloblastoma

Database

Name of gene set (GSEA)

Exploratory dataset(n = 177)

Validation dataset (n = 76)

1000 bootstrapped datasets (n = 253)

Representative core genes**

HR*

p-value

HR*

p-value

% of p-value < 0.05

PID

Notch-mediated HES/HEY network

6.49

< 0.0001

3.35

0.009

100.0

HDAC1,NOTCH1,GATA4,HEY1,TCF3,PARP1,RBBP8,E2F1

TNF receptor signaling pathway

5.31

< 0.0001

5.54

0.000

100.0

FADD,TNFRSF1A,TNFRSF1B,CAV1,IKBKB,GNB2L1,NFKB1

Validated nuclear estrogen receptor α network

8.13

< 0.0001

5.94

0.006

99.9

MYC,HDAC1,XBP1,TRIM59,CCND1,LCOR,UBE2M

EPO signaling pathway

3.50

< 0.0001

3.12

0.012

99.9

CBL,CRKL,INPP5D,NFKB1

Fc-epsilon receptor I signaling in mast cells

4.09

< 0.0001

2.84

0.018

99.9

CBL,GAB2,INPP5D,FCGR2B,IKBKB,NFKB1,FOS

KEGG

Acute myeloid leukemia

4.85

< 0.0001

3.84

0.005

100.0

MYC,AKT3,EIF4EBP1,IKBKB,NFKB1,CCND1

Dorso ventral axis formation

2.68

0.0004

2.82

0.026

99.5

NOTCH1,ETS2,NOTCH2

Antigen processing and presentation

1.71

0.0068

2.10

0.004

95.5

B2M,HSPA1A,HLA-F,TAP2,RFXANK,CD74,PDIA3,HLA-DMA

Nucleotide excision repair

2.22

0.0007

1.40

0.377

93.2

DDB1,POLD4,POLE2,POLE4

One carbon pool by folate

2.09

< 0.0001

1.13

0.635

92.7

GART,MTHFD2L,MTHFD2,TYMS,DHFR

BIOCARTA

Keratinocyte Differentiation

3.29

0.0001

3.32

0.002

100.0

PRKCD,ETS2,TNFRSF1A,TNFRSF1B,IKBKB,NFKB1,FOS

NF-kB Signaling Pathway

2.55

0.0001

2.33

0.004

100.0

MYD88,FADD,TNFRSF1A,TNFRSF1B,IKBKB,IL1R1,NFKB1

HIV-I Nef: negative effector of Fas and TNF

4.71

< 0.0001

3.15

0.011

99.9

PRKCD,FADD,TNFRSF1A,TNFRSF1B,PRKDC,PSEN2, PARP1,NFKB1

NF-kB activation by Nontypeable H. influenzae

5.83

< 0.0001

3.61

0.016

99.8

MYD88,IKBKB,SMAD3,NFKB1

Cell Cycle: G1/S Check Point

2.64

0.0001

3.54

0.009

99.8

CDC25A,HDAC1,TGFB1,CDKN1A,DHFR,CDK1,SMAD3, CDK2,CCND1,E2F1

  1. * Hazard ratio per 0.1 increment in average relative expression of core genes
  2. ** Representative core genes are significantly associated with overall survival (p-value < 0.05) in Cox regression analysis with all samples