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

Table 4 Analysis of gene set over-representation in skeletal muscle in newborn mice.

Category	Count	Ease	% Rescued	Taurine	Average fold change
Category	Count	score	% Rescued	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

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]