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Table 4 Analysis of gene set over-representation in skeletal muscle in 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 967 na 46% na 1 0.98 0.95 0.94
KEGG pathway analysis 263 na 46% na 1 0.99 0.90 0.93
Oxidative phosphorylation 24 5.60E-06 75% 0.010 1 0.92 0.72 1.04
Citrate cycle (TCA cycle) 8 2.45E-03 88% 0.029 1 0.96 0.58 0.93
Valine, leucine and isoleucine degradation 10 4.53E-03 40% 0.757 1 1.02 0.59 0.81
Pyruvate metabolism 9 9.62E-03 67% 0.314 1 0.99 0.49 0.86
Glycolysis / Gluconeogenesis 10 1.12E-02 60% 0.523 1 0.96 0.61 0.98
Panther biological pathways 928 na 46% na 1 0.98 0.94 0.94
Electron transport 65 3.99E-04 45% 1 1 0.96 0.84 0.98
Muscle contraction 13 5.12E-03 64% 0.189 1 0.84 0.38 0.84
Cell adhesion-mediated signaling 33 5.85E-03 52% 0.596 1 0.99 1.06 0.99
Cell motility 48 9.44E-03 44% 0.769 1 1.00 1.16 0.97
Ion transport 133 1.21E-02 53% 0.164 1 0.97 0.94 0.93
GO cellular component 777 na 47% na 1 0.98 0.94 0.94
Mitochondrion 121 2.46E-13 56% 0.065 1 0.97 0.62 0.91
cytoplasmic part 288 8.48E-10 nd nd nd nd nd nd
Cytoplasm 441 1.57E-09 nd nd nd nd nd nd
mitochondrial part 56 4.70E-09 nd nd nd nd nd nd
mitochondrial inner membrane 42 1.12E-07 nd nd nd nd nd nd
  1. Genes found to have their expression level significantly changed in skeletal muscle 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]