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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