Metagenomic next-generation sequencing and proteomics analysis in pediatric viral encephalitis and meningitis

Figure 1. mNGS analysis results of the CSF samples. (A) Total number (besides the bars) of samples with a positive result for each pathogen (x-axis). (B) Comparison of the number of reads between HEV and HHV. (C) Comparison of detection rate between mNGS and PCR analysis. NS, no significant differences.

Figure 2. Comparison of protein expression profiles between patients with encephalitis and normal controls. (A) PCA of whole proteins from proteomics data. (B) Expression heatmaps of differentially expressed proteins. (C) Volcano plot of differentially expressed proteins between two groups: ∣log2FC∣ > 2, FDR < 0.01. (D) The up- and downregulated fold changes (log2) of proteins are colored according to each panel key. (E) Names of the top 10 up- (red) or downregulated (green) proteins between patients with HEV-positive meningitis and normal controls are listed in a bar chart. (F) Comparison of top 10 up- (B1) or downregulated (B2) protein abundance is shown by dot plots between patients with EV-positive encephalitis (red) and normal controls (blue). Relative expression levels (2−ΔΔCt) of these DEPs are shown according to the log scale. Corresponding protein names are listed at the bottom of the chart. *p<0.05, **p<0.01, ***p<0.001.

Figure 3. (A) O-PLS-DA analysis of DEPs between children with with HEV-positive meningitis and normal controls. (B) Top 20 DEPs identified with most importance using O-PLS-DA. (C) Top 20 DEPs identified with P value and FC. (D) 11 DEPs identified with top-ranked P value, FC and VIP scores.

Figure 4. Functional analysis of DEPs between patients with encephalitis and normal controls. (A) GO enrichment bar chart of DEPs presents the number and percentage of DEPs enriched in a biological process (BP), cellular component (CC), and molecular function (MF) between the patients with encephalitis and normal controls. (A1) upregulated expressed proteins; (A2) downregulated expressed proteins. (B) The bubble chart shows the KEGG pathway enrichment analysis of DEPs between two groups. (B1) upregulated expressed proteins; (B2) downregulated expressed proteins. (C) InterPro (IPR) annotation of DEPs between patients with encephalitis and normal controls and the top 10 domain annotations represented in the chart. (D) Subcellular localization of DEPs between patients with encephalitis and normal controls.