PMC

While the total number of DEG decreases from 1-day old worms to 10-day old worms, the fraction of down-regulated genes increase with age under impaired glycolysis.

The MDS was performed using the log2 RPKM values and is based on Pearson correlation between the expression profiles of all samples. Samples are primarily arranged according to age (indicated by color), and only then according to treatment (indicated by shape).

The plot shows the mean RPKM values as well as the standard deviation versus age in days for superoxide dismutase sod-2, the peroxisomal catalase ctl-2 and two genes encoding glutathione peroxidases. Black curve: controls; red curve: DOG-treatment.

The heatmap shows the log2-foldchange for the expression levels of DOG-treated worms and controls. Green color indicates an up-regulation by DOG-treatment, red color indicates a down-regulation by DOG-treatment, compared to controls. A majority of these genes is down-regulated with age by the DOG-treatment. Note especially the strong regulation of mitochondrially encoded genes (starting with MTCE).

Only edges with a weight were drawn. All black edges represent positive weights, i.e. all shown genes exhibit increased co-expression under DOG-treatment. The line width denotes the extent of correlation difference between DOG and DMSO. Several genes present a hub-like structure with a maximum node-degree of 57 for hpo-18 and vha-17. Mitochondrially encoded genes are represented by rectangular shaped nodes, which show less increased co-expression. The node color denotes the assignment to selected GO categories (see legend).

The x-axis shows nine network parameters characterizing the network structure. The ordinate shows the percentage change of the corresponding parameter when DOG feeding replaces standard diet. Note that we plot the percentage change of the reciprocal value of the network diameter, thereby ensuring that upward pointing bars consistently indicate better connectivity under DOG-treatment (compared to controls), and downward-pointing bars indicate relaxed network connectivity in the DOG-case. The colors of the bars indicate the gene set the change was recorded for: grey bars - randomly chosen “background” genes; blue bars - mTOR pathway genes; red bars - oxidative phosphorylation pathway; red bars - glutathione metabolism pathway; green bars - glycolysis pathway.