1. Genes affected concordantly within the ileum and meta-analysis data sets formed biofunctional clusters of overlapping pathways.
Genes affected concordantly within the ileum and meta-analysis data sets formed biofunctional clusters of overlapping pathways. Each node depicts a significantly enriched biological pathway, and each edge depicts overlapping genes that were significantly affected by germ status. Pathways were classified as upregulated if the annotation enrichment was found to be maximally significant by analyzing only the upregulated genes and as downregulated if the annotation enrichment was found to be maximally significant by analyzing only the downregulated genes. (A) The concordant[T,M] network (≥4 overlapping genes per edge) formed three clusters related to cancer (top left), metabolism (top right), and the immune system (top left and bottom center). (B) The concordant[T,P,M] network (with at least one instance of overlapping genes per edge) formed two independent clusters, one composed of downregulated immune system pathways (left) and the other of upregulated metabolic pathways (right).
Nathan P. Manes et al. mSystems 2017; doi: /mSystems