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Fig. 1 | Genome Biology

Fig. 1

From: Host-microbiome protein-protein interactions capture disease-relevant pathways

Fig. 1

Human proteins differentially targeted by the microbiome in disease are enriched for relevant gene-disease associations. A The number of interspecies bacterial protein clusters (blue), human proteins (orange), and interactions (dark blue) in the human-bacteria PPI network; the number of bacterial protein clusters detected in patients from nine metagenomic studies that also have homology to experimentally verified interactors and their putative human interactors; and the number of bacterial clusters and human proteins associated with disease through our metagenomic machine learning approach, by comparing abundances in cases (gray) and control (red). B Proportions of human proteins implicated in disease, according to their GDAs (GDAs > 0.1) in DisGeNET, within: all reviewed human proteins; HBNet; human interactors with detected bacterial proteins; and those human interactors with feature importances above the 90th percentile in their respective cohorts. p values for enrichments are depicted by: * p<0.05; ** p<0.01; *** p<10−3; **** p<10−4 (chi-square test). Total numbers of each set are noted in the legend. C Human cellular pathways (annotated by IPA) enriched in the set of human proteins within HBNet (left) and those detected across all nine metagenomic case-control studies (right) colored according to their Benjamini-Hochberg false discovery rate (BHFDR)-adjusted p value. Only those pathways with BHFDR-adjusted < 0.05 in the disease-associated sets are shown. p values for enrichments are depicted by: * p<0.05; ** p<0.01; *** p<10−3; **** p<10−4 (Fisher’s exact test). D 106 species (left) with experimentally verified proteins in 3056 bacterial protein clusters are mapped to 821 bacterial species (right) with homologs detected in patients’ metagenomes (right), representing a total of 1698 clusters. Species are colored according to phylum

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