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