Fig. 6
A Deconvolution results for fibroblasts and proximal tubular cells in two Visium kidney fibrosis samples using CellTrek [50]. CellTrek maps single cells to spatial locations through coembedding and metric learning approaches. B Spot-level deconvolution results for fibroblasts and proximal tubular cells. Using the single-cell level deconvolution with CellTrek, we aggregate to achieve spot-level deconvolution. C In line with previous studies [49], pathway enrichment analysis using niche-DE marker genes in fibroblasts near proximal tubular cells as input finds ECM organization, platelet activation, and collagen formation as top processes. D Ligand-receptor pairs found between fibroblasts and proximal tubular cells via niche-LR include APP/CD74, JAG1/NOTCH1, and CX3CL1/CX3CR1. In particular NOTCH signaling is known to be induced in fibrosis [49]