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Fig. 3 | BMC Bioinformatics

Fig. 3

From: Searchlight: automated bulk RNA-seq exploration and visualisation using dynamically generated R scripts

Fig. 3

A selection of the default outputs from the differential expression workflow, using the demonstration dataset. Comparison of Lamina Propria (LP) to Mesenteric Lymph (ML). Significance for differential genes was adjusted p < 0.01 and absolute log2 fold change > 1. Upregulated genes are higher in ML. a Bar chart of the number of up and downregulated genes. b MA plot. Significant genes are red and non-significant black. c Volcano plot. Significant genes are red and non-significant black. d Gene expression heatmap for the 2342 significantly differential genes. Colour denotes row scaled (Z-score) expression values, with darkest blue as lowest expression and darkest red as highest. The Y-axis has been hierarchically clustered using Spearman Correlations, UPMG agglomeration and mean reordering. e Table of the 5 most upregulated genes by p value. f Gene expression violin and jitter plots for each of the two most significantly upregulated genes in ML. Black dots denote individual samples. The red dot and whisker denote mean and standard deviation respectively. g Bar chart of the five most enriched gene-sets (GO Biological Processes). The X-axis shows the − log10 p value and the data labels the number of significant genes in each gene-set. h Bar chart of the five most inhibited upstream regulators (TRRUST). The X-axis shows the activation Z-score and the data labels the number of significant genes associated with each activator. i Gene expression boxplots for each gene in the enriched gene-set Adaptive Immune Response. Expression levels are given as per gene Z-scores. Boxes of LP samples are red, and ML are blue. j Network plot of the significantly enriched (adjusted p < 0.05) upstream regulators. Nodes denote regulators and edges join nodes where > 50% of the regulated genes are shared. Colour intensity represents significance (− log10p) and node size the number of regulated genes

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