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. 2020 Sep 25;7:565530. doi: 10.3389/fmolb.2020.565530

Figure 1.

Figure 1

Overview of entire RNA-Seq data analysis workflow and volcano plots for dynamically expressed genes. Plots were constructed using the EnhancedVolcano (Blighe, 2019) package in R. Horizontal lines are drawn at p = 0.001. Vertical lines are added at log2 fold change values of 1 and −1. DESeq2's shrunken log2 fold change metric was used. Genes with significant differential expression (p < 0.001 and LFC >1 or LFC < −1) are colored red. (A) Flowchart of steps used to analyse RNA sequencing data obtained from mice of different age groups. Data preparation steps are colored in light blue, differential expression analysis steps are colored in pink, and downstream analysis steps are colored in purple. (B) Results of the likelihood ratio test using a reduced model with sex as the sole explanatory variable; genes identified as significant (red) vary in expression with age. (C) Results of the Wald test comparing gene expression in the 4 week group to expression in the 15 week group. (D) Results of the Wald test comparing gene expression in the 15 week group to expression in the 8 month group. (E) Results of the Wald test comparing gene expression in the 8 month group to expression in the 22 month group. This comparison identified the largest number of transcripts with p < 0.05 of the three pairwise comparisons.