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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.
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BMC Bioinformatics

ISSN: 1471-2105

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