Fig. 4: Integrated analysis of scRNA-seq and Visium. | Communications Biology

Fig. 4: Integrated analysis of scRNA-seq and Visium.

From: Inflammation-associated molecules in the glomerular-endothelium in mild IgA-nephropathy patients identified by single-cell and spatial transcriptome

Fig. 4

Spots detected from histological images of normal specimens and IgA-N specimens. a Detected spots classified by a pathologist into the following four regions according to their histological features: cortex, medulla, glomeruli (Glom), and other. b Dot plots showing the expression of glomerular constituent cell marker genes (podo; NPHS1, mesa; PDGFRA, GE; EHD3) in each region. (c) UMAP plots of the clusters used for integrated analysis with Visium: GE, Cluster #18; and endothelial cells (Endo) (Endo1, Cluster #2; Endo2, Cluster #13; Endo3, Cluster #15; Endo4, Cluster #17; and Endo5, Cluster #27). Gray dots indicate cells not used for the integrated analysis with Visium. Predictive score of each cell type (scRNA-seq data; X-axis) against each histological annotation (Visium data; Y-axis) of (d) normal specimens and (e) IgA-N specimens. The dot color represents the scaled predictive score, and the dot size represents the proportion of spots with a predictive score of >0 in each histological annotation. IgA immunoglobulin A, scRNA-seq single-cell RNA sequencing UMPA uniform manifold approximation and projection.

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