Fig. 3: CR and RM induce distinct gene expression signatures.
From: Distinct and additive effects of calorie restriction and rapamycin in aging skeletal muscle
A Scheme of treatment groups, muscles, and numbers of samples used in sequencing analysis. Data for 10mCON, 30mCON, and 30mRM have been previously reported13. B Coordinates of principal components representing aging (PC3 for 10mCON and 30mCON) CR (PC4 for 30mCON and 30mCR), RM (PC4 for 30mCON and 30mRM) and CR vs. RM (PC3 for 30mCR and 30mRM) effects for gene expression collected in soleus (SOL), tibialis anterior (TA), triceps brachii (TRI) and gastrocnemius (GAS). The fraction of variance in gene expression and the number of genes aligned (Pearson correlation coefficient ≥0.4, z score projection ≥1.96) with each PC is displayed for each comparison. C Pairwise Venn diagram comparisons of genes significantly aligned to aging, CR and RM effects. Numbers in red, blue and black represent increasing, decreasing and oppositely regulated genes, respectively, with level of significance and representation factor denoted. D Top-ten DAVID gene ontology terms enriched (P < 0.05; gray and red dashed lines; one-sided, modified Fisher’s exact test) for genes aligned to both aging and CR effects, aging and RM effects or CR and RM effects. E Heatmap of fold-changes for genes aligned with any of the four PCs described in B for all four muscles. Hierarchical clustering based on the Euclidean distance of these changes rendered 8 gene clusters. n = 6 mice per muscle per group, except for SOL 30mCON where one data point was removed due to a technical error. F Plasma cytokine protein concentration; n = 6 (10mCON), 8 (30mCON), 6 (30mCR) and 6 (30mRM). Data are mean ± SEM and displayed as fold-change from 10mCON group. Cytokine levels below the fit curve range were set as 0. A one-way ANOVA with Fishers post hoc test was used to make comparisons between 10mCON and 30mCON, 30mCON and 30mRM and 30mCON and 30mCR. *, **, and *** denote a significant difference between groups of P < 0.05, P < 0.01, and P < 0.001, respectively. Where 0.05 < P < 0.10, P values are reported. Experimental scheme in A created with BioRender.com.
