Fig. 6: scRNAseq - hierarchical cluster and analysis of individual myeloid clusters with significant differences between the BCG- and ΔsigH-vaccinated groups. | Nature Communications

Fig. 6: scRNAseq - hierarchical cluster and analysis of individual myeloid clusters with significant differences between the BCG- and ΔsigH-vaccinated groups.

From: Prevention of tuberculosis in cynomolgus macaques by an attenuated Mycobacterium tuberculosis vaccine candidate

Fig. 6

a tSNE visualization of reclustered myeloid cells (all conditions together). b Bubble plot and (c) violin plot depicting expression of canonical marker genes used for identification of myeloid cell populations. d–e Bubble plots focused on two key myeloid clusters, Mac-IFN and pDCs, show the expression of selected significant markers within each cluster, highlighting differences in expression levels across various groups. Cluster-specific markers were identified using Wilcoxon rank-sum tests, with Bonferroni correction for multiple hypothesis testing. Parameters: only.pos = TRUE, min.pct = 0.25, logfc.threshold = 0.25. f Expression of IFN-related genes across groups. g–h Significant Hallmark pathways showing differences in Mac-IFN cluster between groups 3 vs 2 (g) and groups 3 vs 4 (h) in cluster Mac-IFN. Pathway analyzes are based on permutation test for independence from the fgsea R package using the Molecular Signatures Database (MSigDB) for human hallmark gene sets. Benjamini-Hochberg corrections for multiple hypothesis testing with FDR < 0.05.

Back to article page