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Table 5 Connecting CS transcriptional modules to enriched biological pathways (p-value < 0.01)

From: Comparative analysis of acute and chronic corticosteroid pharmacogenomic effects in rat liver: Transcriptional dynamics and regulatory structures

Transcriptional modules Enriched biological pathways p-value GRE+
1 Nitrogen metabolism(rno00910) 0.0000313 X
  Glycine, serine and threonine metabolism(rno00260) 0.0006195 x
  Bisphenol A degradation(rno00363) 0.0009858
  Tryptophan metabolism(rno00380) 0.0013596 x
  Histidine metabolism(rno00340) 0.0017470
  beta-Alanine metabolism(rno00410) 0.0020365
  Bile acid biosynthesis(rno00120) 0.0027013
  Arachidonic acid metabolism(rno00590) 0.0053445  
  Pantothenate and CoA biosynthesis(rno00770) 0.0056735
  Butanoate metabolism(rno00650) 0.0072639
  Tyrosine metabolism(rno00350) 0.0079428
  Valine, leucine and isoleucine degradation(rno00280) 0.0094101
2 Tyrosine metabolism(rno00350) 0.0000590
  Aminophosphonate metabolism(rno00440) 0.0001267 x
  Selenoamino acid metabolism(rno00450) 0.0004668 x
  Histidine metabolism(rno00340) 0.0010152 x
  Alanine and aspartate metabolism(rno00252) 0.0013658
  Arginine and proline metabolism(rno00330) 0.0019112
  Tryptophan metabolism(rno00380) 0.0040672 x
  Androgen and estrogen metabolism(rno00150) 0.0042813 X
3 Oxidative phosphorylation(rno00190) 9.000E-08 x
  Androgen and estrogen metabolism(rno00150) 0.0000888  
  Starch and sucrose metabolism(rno00500) 0.0020632  
  Urea cycle and metabolism of amino groups(rno00220) 0.0069082  
  Pentose and glucuronate interconversions(rno00040) 0.0076060  
4 Ribosome(rno03010) 0.000E+00  
  Proteasome(rno03050) 0.0000037 X
5 None   
6 Proteasome(rno03050) 2.570E-04 x
  Tight junction(rno04530) 3.410E-04 x
  Long-term depression(rno04730) 4.090E-04 x
  TGF-beta signaling pathway(rno04350) 5.040E-04 x
  Wnt signaling pathway(rno04310) 0.0032164 X
  1. +: Glucocorticoid Receptor Element - GRE binding sites; √: GRE binding sites are present on the promoters of almost all genes in the corresponding function group; x: possibly because of not enough promoter information to be considered. Details are listed in functional characterization in Additional File 3.