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Table 3 Top three pathways for overrepresentation in each tissue

From: Differential gene expression in liver and small intestine from lactating rats compared to age-matched virgin controls detects increased mRNA of cholesterol biosynthetic genes

Liver    
Pathway Fisher's Exact test p-value BH p-value Members
Biosynthesis of steroids 3.50E-07 5.80E-05 ↑Dhcr7, ↑Fdft1,↑Hmgcr,↑Idi1, ↑Lss, ↑Mvd, ↑Sqle
LXR/RXR Activation 1.57E-04 1.30E-02 ↓Abcg5, ↓Abcg8, ↑Acaca, ↑Cyp7a1, ↓Hadh, ↑Hmgcr, ↓Lcat
Pentose/Phosphate Pathway 3.01E-04 1.67E-02 ↑Aldoc, ↑G6pd, ↑Gpi, ↓H6pd, ↓Pgm5
Duodenum    
Pathway    
Biosynthesis of steroids 1.13E-10 1.74E-08 ↑Dhcr7, ↑Fdft1, ↑Fntb, ↑Hmgcr, ↑Idi1, ↑Lss, ↑Mvd, ↑Sc5dl, ↑Sqle
Androgen and estrogen metabolism 1.35E-04 1.04E-02 ↑Ftsj1, ↑Hsd11b1, ↑Hsd17b7, ↑Nsdhl, ↓Srd5a2, ↓Ugt2b7
Glycerolipid metabolism 1.46E-03 7.50E-02 ↓Cel, ↓Clps, ↓Glb1l2, ↓Pnlip, ↓Pnliprp1, ↓Pnliprp2
Jejunum    
Pathway    
T-Cell receptor signaling 1.68E-07 2.78E-05 ↓Bmx, ↓Cd8b, ↓Grap2, ↓Itk, ↓Malt1, ↓Pik3cg, ↓Pik3r1, ↓Ppp3cc, ↓Prkcq, ↓Ptprc, ↓Rasgrp1, ↓Trb
CD28 signaling in T helper cells 1.17E-05 6.74E-04 ↓Grap2, ↓Itk, ↓Malt1, ↑Mapk9, ↓Pik3cg, ↓Pik3r1, ↓Ppp3cc, ↓Prkcq, ↓Ptprc, ↓Trb
TR/RXR activation 1.23E-05 6.74E-04 ↑Fga, ↑Gh1, ↓Klf9, ↑Ldlr, ↓Pik3cg, ↓Pik3r1, ↓Thra, ↓Thrb, ↓Thrsp
Ileum    
Pathway    
Biosynthesis of steroids 9.42E-08 1.71E-05 ↑Cyp24a1, ↑Dhcr7, ↑Fdft1, ↑Hmgcr, ↑Idi1, ↑Mvd, ↑Sc5dl, ↑Sqle
TR/RXR activation 3.16E-07 2.86E-05 ↑Fga, ↑Gh1, ↓Klf9, ↑Me1, ↓Nfcor2, ↓Pck1, ↓Pik3c2b, ↓Pik3cg, ↓Pik3r5, ↓Ppargc1a, ↓Thra, ↓Thrb
Thrombopoietin signaling 4.85E-05 2.53E-03 ↓Irs2, ↓Pik3c2b, ↓Pik3cg, ↓Pik3r5, ↓Plcg1, ↓Plcg2, ↓Prkce, ↓Prkcq
  1. The pathways with the three lowest p-values from Fisher's exact test for pathways from IPA's "Canonical Pathways" database for each tissue are reported here along with the corresponding p-value from a right-tailed Fisher's exact test, the Benjamini-Hochberg (BH) adjusted p-value, and the genes within the pathway that showed differential expression within the respective tissue (Members). Arrows in the Members column indicate the direction of change in lactating animals relative to controls.
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BMC Genomics

ISSN: 1471-2164

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