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Fig. 5 | Microbiome

Fig. 5

From: Gut microbiome signatures linked to HIV-1 reservoir size and viremia control

Fig. 5

Baseline functional enrichment in levels of immune activation and inflammatory response in viremic controllers. a Volcano plot of differentially expressed genes between controllers and non-controllers at baseline (pre-Vax) with adjusted p value < 0.1 (violet dots), adjusted p value < 0.05 (red dots) and log2 (foldchange) > 2 and adjusted p value < 0.05 (green dots). Gray-colored dots represent genes not displaying statistical significance (BH-adjusted p value > 0.1). The log2 fold change on the x-axis indicates the magnitude of change, while the −log10 (p-adjust) on the y-axis indicates the significance of each gene. b Violin plots showing relative expression levels (rlog, regularized log transformation) of differentially expressed genes with functional annotation. c Gene ontology (GO) enrichment analysis of upregulated genes in controllers. In the y-axis, only representative enriched GO terms (biological process) are reported (terms obtained after redundancy reduction by REVIGO). X-axis reports the percentage of genes in a given GO terms, expressed as ‘Gene ratio’. The color key from blue to red indicates low to high Bonferroni-adjusted log 10 p value. Dot sizes are based on the 'count' (genes) associated to each GO term. Significantly enriched GO terms, number of genes associated with each GO term and adjusted p values are provided in Additional file 3: Table S3

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