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Fig. 5 | Genome Biology

Fig. 5

From: tmap: an integrative framework based on topological data analysis for population-scale microbiome stratification and association studies

Fig. 5

Systematic analysis of interrelations between taxa and host covariates of the FGFP microbiomes. a PCA (principal component analysis) of the SAFE scores of taxa and host covariates shows the overall pattern of their associations with microbiome. The top 10 covariates and taxa identified by SAFE enriched scores are highlighted (markers with edge color of gray) and annotated with their names. Host covariates are colored based on metadata category, and taxa are in red. Marker size is scaled according to the SAFE enriched score of metadata or taxa. b, c Co-enrichment networks of gender and other co-enriched host covariates and taxa, for female and male respectively. The networks reveal the interrelations between gender and other covariates or taxa when considering their associations with the FGFP microbiomes. Edge width of the network is scaled according to the negative log-transformed p value of Fisher’s exact test of co-enrichment. Color and size of the nodes are the same as that of PCA plot. d Co-enrichments between disease and medication. For instance, ulcerative colitis is co-enriched with six different drugs. On the other hand, amoxicillin and enzyme inhibitor (J01CR02) is co-enriched with three different diseases. Colors are based on their co-enrichment subnetworks. e Subnetworks of disease-medication co-enrichments. The identified co-enrichments are highlighted in the TDA network of the FGFP microbiomes with different colors. Co-enrichment relations of a same color indicates that they are co-enriched in a same subnetwork

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