Fig. 8: “Pseudo-bulk” DE analysis combining all samples from patients recruited in Cali and Tumaco has relevant overlap with predictive features identified by ML.
From: Innate biosignature of treatment failure in human cutaneous leishmaniasis
PCA for all samples collected from patients in Cali and Tumaco (Mo, Nϕ, and Eϕ, collected Pre-Tx, Mid-Tx, and at End-Tx) were performed using log2 transformed, quantile and CPM-normalized, and filtered counts of annotated protein-coding genes (A), SVA-adjusted data considering cell-type for variance adjustment (B). The first two PCs are shown on the X and Y-axes, with the proportion of total variance attributable to that PC indicated. The inner and outer colored ellipses represent the 90% and 95% confidence intervals, respectively. C Volcano plot of DEGs, using DEseq (Wald test and its Benjamini-Hochberg adjusted P-value < 0.05 and |log2FC | ≥ 1), highlighting in labels the top 10 up- or down-regulated genes in TF compared to cures.
