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Table 2 PANTHER analysis of differentially expressed genes by pathway.

From: Tight regulation of wingless-type signaling in the articular cartilage - subchondral bone biomechanical unit: transcriptomics in Frzb-knockout mice

Pathway number of genes in reference list number of regulated genes Expected number of genes P-value*
Pathways that are overrepresented taking up-regulated genes into account
Integrin signaling pathway 185 19 3.48 4.78E-09
WNT signaling pathway 348 22 6.55 1.27E-06
Angiogenesis 193 12 3.63 3.76E-04
Cadherin signaling pathway 167 11 3.14 4.07E-04
Alzheimer disease-presenilin pathway 124 9 2.33 6.84E-04
Pathways that are overrepresented taking downregulated genes into account
B cell activation 87 21 3.01 1.03E-11
p53 pathway 127 18 4.39 8.32E-07
Inflammation mediated by chemokine and cytokine signaling pathway 298 29 10.30 1.12E-06
Blood coagulation 55 10 1.90 2.96E-05
p53 pathway feedback loops 2 51 9 1.76 9.15E-05
Parkinson disease 106 13 3.66 1.13E-04
Cell cycle 24 6 0.83 2.21E-04
Integrin signaling pathway 185 17 6.39 3.38E-04
De novo pyrimidine deoxyribonucleotide biosynthesis 23 5 0.79 1.36E-03
DNA replication 25 5 0.86 1.95E-03
Ras Pathway 80 9 2.76 2.20E-03
Apoptosis signaling pathway 141 12 4.87 4.37E-03
T cell activation 142 12 4.91 4.61E-03
JAK/STAT signaling pathway 20 4 0.69 5.48E-03
Angiogenesis 193 14 6.67 8.51E-03
Pathways that are overrepresented taking up- and down-regulated genes into account
Integrin signaling pathway 185 36 9.87 7.87E-09
B cell activation 87 24 4.64 7.10E-09
Inflammation mediated by chemokine and cytokine signaling pathway 298 41 15.90 2.42E-06
p53 pathway 127 21 6.78 1.79E-04
Angiogenesis 193 26 10.30 4.45E-04
Blood coagulation 55 12 2.93 8.00E-04
p53 pathway feedback loops 2 51 9 2.72 2.42E-02
Cell cycle 24 6 1.28 2.19E-02
WNT signaling pathway 348 31 18.57 4.57E-02
Axon guidance mediated by netrin 29 6 1.55 4.36E-02
Parkinson disease 106 13 5.66 4.22E-02
  1. * P-values are obtained by the binomial test; only P-values that fulfilled an additional false discovery rate test are shown.