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Table 2 Pathways enriched in temporal patterns by SST

From: Sho-saiko-to, a traditional herbal medicine, regulates gene expression and biological function by way of microRNAs in primary mouse hepatocytes

   Pathways from temporal up-pattern (KEGG ID) P-value* FDR** Pathways from temporal down-pattern (KEGG ID) P-value FDR
All genes Simple enrichment analysis Cell cycle (mmu04110) 8.41E-05 9.62E-03 Drug metabolism-cytochrome P450 (mmu00982) 3.57E-10 3.07E-08
Systemic lupus erythematosus (mmu05322) 7.97E-10 3.43E-08
Complement and coagulation cascades (mmu04610) 3.45E-08 9.88E-07
Retinol metabolism (mmu00830) 4.38E-08 9.41E-07
Metabolism of xenobiotics by cytochrome P450 (mmu00980) 1.15E-06 1.97E-05
Linoleic acid metabolism (mmu00591) 2.04E-06 2.92E-05
Prion diseases (mmu05020) 2.43E-05 2.99E-04
PPAR signaling pathway (mmu03320) 3.42E-05 3.67E-04
Drug metabolism-other enzymes (mmu00983) 4.87E-04 4.64E-03
Topology-based signaling pathway analysis     Systemic lupus erythematosus (mmu05322) 1.74E-10 1.36E-08
Complement and coagulation cascades (mmu04610) 4.55E-10 1.77E-08
Cytokine-cytokine receptor interaction (mmu04060) 1.69E-08 1.84E-06 Prion diseases (mmu05020) 2.82E-07 7.33E-06
Osteoclast differentiation (mmu04380) 4.88E-06 2.66E-04 PPAR signaling pathway (mmu03320) 1.42E-06 2.78E-05
Cell cycle (mmu04110) 1.52E-04 5.55E-03 Staphylococcus aureus infection (mmu05150) 3.48E-06 5.42E-05
    Serotonergic synapse (mmu04726) 1.18E-05 1.53E-04
Alcoholism (mmu05034) 2.48E-04 2.77E-03
Endocrine and other factor-regulated calcium reabsorption (mmu04961) 7.76E-04 7.57E-03
MicroRNA targets Simple enrichment analysis No pathway    Metabolism of xenobiotics by cytochrome P450 (mmu00980) 1.45E-04 3.19E-03
Topology-based signaling pathway analysis Cell cycle (mmu04110) 5.46E-03 1.00E-02 No pathway   
Non-microRNA targets Simple enrichment analysis No pathway    Systemic lupus erythematosus (mmu05322) 1.63E-10 1.22E-08
Complement and coagulation cascades (mmu04610) 9.24E-09 3.46E-07
Drug metabolism (mmu00982) 1.94E-07 4.85E-06
Prion diseases (mmu05020) 1.20E-05 2.26E-04
Retinol metabolism (mmu00830) 2.82E-05 4.22E-04
Linoleic acid metabolism (mmu00591) 2.01E-04 2.51E-03
PPAR signaling pathway (mmu03320) 8.76E-04 9.34E-03
Topology-based signaling pathway analysis Cytokine-cytokine receptor interaction (mmu04060) 1.63E-07 1.42E-05 Systemic lupus erythematosus (mmu05322) 3.95E-11 3.00E-09
Complement and coagulation cascades (mmu04610) 1.31E-10 4.97E-09
Prion diseases (mmu05020) 1.32E-07 3.34E-06
NF-kappa B signaling pathway (mmu04064) 2.37E-05 8.95E-04 Staphylococcus aureus infection (mmu05150) 1.63E-06 3.10E-05
MAPK signaling pathway (mmu04010) 3.09E-05 8.95E-04 Serotonergic synapse (mmu04726) 5.15E-05 7.83E-04
Osteoclast differentiation (mmu04380) 4.17E-04 9.07E-03 PPAR signaling pathway (mmu03320) 9.33E-05 1.18E-03
Endocrine and other factor-regulated calcium reabsorption (mmu04961) 6.65E-04 7.22E-03
      Alcoholism (mmu05034) 9.07E-04 8.61E-03
  1. *For simple enrichment analysis, the p values are calculated by the Fisher’s exact test in the DAVID program [30]. For topology-based signaling pathway analysis, the p value indicates the global pathway significance p value (PG), which combines the enrichment p values and the perturbation p values in regard to pathway topology with a random bootstrap iteration number of 3000 [31].
  2. **The false discovery rate (FDR) correction is measured by applying the Benjamini algorithm [30, 31].