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Table 3 Analysis of gene set over-representation in liver newborn mice.

From: A maternal low protein diet has pronounced effects on mitochondrial gene expression in offspring liver and skeletal muscle; protective effect of taurine

Category Count Ease % Rescued Taurine Average fold change
score score NP NP+tau LP LP+tau
All genes 2012 na 30% na 1 0.96 0.95 0.96
KEGG pathway analysis 620 na 31% na 1 0.97 1.02 1.01
Oxidative phosphorylation 42 1.56E-06 43% 0.125 1 1.06 1.44 1.21
Valine, leucine and isoleucine degradation 17 3.13E-03 24% 0.604 1 1.04 1.47 1.27
Lysine degradation 17 4.12E-03 41% 0.428 1 1.02 1.40 1.24
Butanoate metabolism 15 2.04E-02 27% 1 1 0.99 1.16 1.19
Limonene and pinene degradation 10 2.06E-02 20% 0.732 1 0.98 1.15 1.14
Panther biological pathways 1965 na 30% na 1 0.96 0.95 0.96
Fatty acid metabolism 122 7.90E-05 40% 0.027 1 0.95 0.86 0.94
Protein disulfide-isomerase reaction 90 1.16E-04 29% 0.907 1 0.99 1.04 1.01
Oxidative phosphorylation 175 1.63E-03 28% 0.606 1 0.94 0.97 0.97
Immunity and defense 171 2.34E-03 30% 1 1 0.99 0.86 0.95
Carbohydrate metabolism 86 4.54E-03 32% 0.722 1 0.97 1.07 1.05
GO cellular component 1627 na 30% na 1 0.96 0.95 0.96
mitochondrion 209 4.71E-11 37% 0.057 1 1.03 1.29 1.13
Cytoplasm 866 4.53E-08 nd nd nd nd nd nd
Intracellular part 1231 2.51E-07 nd nd nd nd nd nd
mitochondrial inner membrane 68 1.21E-06 nd nd nd nd nd nd
organelle inner membrane 69 3.63E-06 nd nd nd nd nd nd
  1. Genes found to have their expression level significantly changed in liver in newborn mice subjected to a maternal low protein diet compared to a normal diet were examined for over-representation of specific gene sets as described. The top 5 most significant over-represented gene sets are shown. Count) Total number of genes in analysis. Ease score) a modified fishers exact test describing the probability of gene set enrichment. % Rescued) Amount of rescued or partially rescued genes (see table 2 and materials and methods) in percent of count. Taurine score) Fishers exact test examining if taurine preferentially rescued the gene set compared to the rescue effect seen in all genes examined in the parent geneset. Average fold change) Means of fold change for the 4 diet groups per gene set in regard to NP. NP) normal protein (20% casein) or LP) low protein (8% casein) during pregnancy, tau) 1% taurine supplementation in the drinking water during pregnancy. na) not applicable. nd) not determined. Table reprinted with permission from Wolters Kluwer Health / Lippincott Williams & Wilkins. [52]