Geometry of the Gene Expression Space of Individual Cells
Fig 3
Expression profiles of the four colon crypt archetypes are each enriched for markers of specific cell types.
(a) The expression profiles of the four archetypes, with enriched genes colored. Enriched genes were determined by leave-1-out enrichment analysis, binning the cells according to distance from each archetype and seeking when average expression in the bin closest to the archetype is maximal, as described in Methods: 1D Gene enrichment at archetypes (See full enriched genes list in S2 Table). Light blue—enterocyte archetype, yellow—Nodal archetype, green—stem cells archetype, red—goblet cell archetype. Genes that are not enriched, or enriched in more than one archetype, are in dark blue. Zero level represents the average expression of each gene in the dataset. (b) Leave-1-out enrichment plot: expression of a gene (SLC26A3—an enterocyte marker) as a function of distance from archetype in equal mass bins of cells (Methods: 1D Gene enrichment at archetypes), line color indicates archetype. This gene is maximally enriched only at the enterocyte archetype (blue line). For enrichment plots for additional genes see S5 Fig. (c) A two dimensional enrichment plot of SLC26A3, in which its expression is plotted on the plane of the first 2PCs of the data, indicating expression is maximal in the cells closest to the enterocyte archetype. Contours are expression density estimated using a Gaussian kernel (Methods: 2D Gene enrichment at archetypes). Archetype positions and PCs were calculated without the tested gene.