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Fig. 5 | BMC Bioinformatics

Fig. 5

From: BEAVR: a browser-based tool for the exploration and visualization of RNA-seq data

Fig. 5

Visualizing normalized read counts and differential gene expression between experimental groups. a Normalized read count plots are shown for ten embryonic stem cell-like genes of interest from the Sehrawat et al. dataset to illustrate changes between the DMSO- and SP2509-treated groups. BEAVR allows users to enter a list of genes to illustrate expression behavior as jitter plots (shown) or boxplots (not shown). A 5 × 2 (rows x columns) grid was selected to display these 10 genes. b The top 50 most differentially-expressed genes between DMSO- and SP2509-treated groups are shown in the clustered heatmap for the Sehrawat et al. dataset. This heatmap was generated in the Heatmap tab using the Ward.D2 hierarchical clustering method and Euclidean distance measurements. Row (gene) clustering was enabled. Clustered heatmaps are useful for displaying expression changes across treatment groups. c A volcano plot highlighting genes that meet both LFC and padj cutoffs are shown for the Sehrawat et al. dataset. This volcano plot was generated in the Volcano Plot tab with the LFC cutoff set to ±1 and the padj cutoff set to < 0.05. The volcano plot is another way to visualize the data shown in the heatmap in (b), however the volcano plot also illustrates the statistical significance of genes (the y-axis)

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