Extended Data Fig. 5: Multicellular neighbourhood and community interactions across the intestine.

A) Schematic of a representative community map and corresponding tissue community network graph (one of 64 tissues). B-C) Community-community motifs that are significantly enriched in both the small intestine and colon as compared to a null distribution of motif instances created from random permutation of tissue graph labels, where B) shows only those motifs that interact with the Adaptive Immune Enriched community and C) shows all other shared motifs between the SB and CL. Motifs indicated by shape and colour indicate those motifs that have significant p value versus those that are indicated with an x in the graph; p values were Bonferroni corrected by multiplying by twice the number of tests conducted in each comparison group. Colour legend is also the same as panel B. D) Representative neighbourhood map (one of 64 tissue sections from 8 donors) with (scale bar = 500 µm) E) Region magnified as in the main figure of the mucosal area of a colon community map, but this time with the multicellular neighbourhoods coloured (see panel D for legend) (scale bar = 100 µm). F) Spatial context maps of the CL highlighting relationships of multicellular neighbourhoods across just the neighbourhoods found within the tissue unit Mucosa. This structure is defined by the number of unique neighbourhoods required to make up at least 85% in a given window. Circles represent the number of cells represented by a given structure. Red rectangle highlights a structure discussed in the manuscript and maps this structure back to panel K. Colour legend is also the same as panel D. G-H) Cell type percentage of G) epithelial and H) stromal cells shown for each community ordered in relative order of general increasing proximity to the lumen based on community spatial context analysis.