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Fig. 5 | BMC Bioinformatics

Fig. 5

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

Fig. 5

Results from re-analysis of dataset 1 [20] (GEO ID: GSE97358). Comparison between control and TGFB1 treated primary cardiac fibroblasts using Searchlight. Significance for differential expression was adjusted p < 0.05 and absolute log2 fold > 1. Upregulated genes are higher in TGFB1 treated. a PCA scatter plots, showing PC1 versus PC2 (top plot) and PC3 versus PC4 (bottom plot). The percent variation is given on the axis label. b Volcano plot of control versus TGFB1. Significant genes are labelled and in red. c Gene expression violin plots for each of the four most significantly differential genes. Significance at p < 0.05 and absolute log2 fold > 1 is denoted by an asterisk. Black dots denote individual samples. The red dot and whisker denote mean and standard deviation respectively. d Network plot of the enriched (adjusted p < 0.05) gene-sets (GO Biological Processes) for the 737 significant genes. Nodes denote gene-sets and edges join nodes where > 50% of the genes are shared. Node colour intensity represents enrichment (− log10 p value) and node size the number of significant genes in the gene-set. Representative names for node clusters are given

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