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. 2016 Feb 16;6:20127. doi: 10.1038/srep20127

Figure 2. Gut microbiome affects the hepatic transcriptome and the daily hepatic gene expression.

Figure 2

(a) Hepatic transcriptome was analysed at ZT0, ZT6, ZT12, and ZT18 in GF and SPF mice using Affymetrix Mouse Gene 2.0 ST arrays. Each group comprised 5 mice (a total of 40 animals). A model was fitted using the limma lmFit function. Probes with FDR < 1% (BH procedure) were considered significantly regulated. A hierarchical clustering was obtained from individual’s expression values of 4429 significantly regulated ProbeSets overall comparisons using 1-Pearson correlation coefficient as distance and the Ward’s criterion for agglomeration. Red and green colors presented in the heatmap indicate values above and below the mean centred and scaled expression values, respectively. Black indicates values close to the mean. The ProbeSets clustering and individuals clustering are illustrated on left panel dendrogram and top panel dendrogram, respectively. (b) Gene expression profiles of the 9 ProbeSets clusters. Mean expression values centred and scaled (average Z-score) are plotted for each sanitary status along the Zeitgeber time (ZT) (GF, black line and SPF, black dotted line). Data are scaled so that values for SPF mice at ZT0 equal zero (reference group). Error bars represent the 95% confidence interval (n = 5 animals/group/ZT time point). (c) Rhythmicity analysis (JTK_Cycle) on ProbeSets. For each ProbeSets cluster, the rhythmicity classes distribution is illustrated as pie charts. ProbeSets are categorized into 6 classes according to rhythmicity significance and parameters (period and phase lag) results regarding SPF and GF mice. Class 1 (dark grey): significant rhythmic ProbeSets with identical rhythmicity parameters for both SPF and GF mice; Class 2 (dark blue): significant ProbeSets in both SPF and GF mice but with a phase lag for GF mice; Class 3 (blue): significant rhythmic ProbeSets in both SPF and GF mice but with a different period for GF mice; Class 4 (light blue): significant rhythmic ProbeSets in SPF but not in GF mice; Class 5 (beige): significant rhythmic ProbeSets in GF but not in SPF mice; Class 6 (light grey): no significant rhythmic ProbeSets neither in SPF nor in GF mice.