Supplementary Figure 8: Spatial expression patterns identified in spatial transcriptomics breast cancer data. | Nature Methods

Supplementary Figure 8: Spatial expression patterns identified in spatial transcriptomics breast cancer data.

From: Identification of spatial expression trends in single-cell gene expression data

Supplementary Figure 8

(A) Spatial expression patterns of significant genes (by at least one of the four statistical tests, Benjamini-Hochberg adjusted P < 0.05, two-sided) for spatial-transcriptomics breast-cancer dataset (layer 2, n=251 array-spots). Expression levels were scaled to the range [0-1] for visualisation purposes. Red circles in the density plots (B) indicate cells in regions with significantly higher expression (one-sided kernel density estimation, P ≤ 0.05). (C) Heatmap with genes by row and cells by column, where black indicate that a cell was deemed by trendsceek to be in a region of significantly upregulated expression. Upper bar indicates cell-clusters and left bar gene-clusters (agglomerative hierarchical clustering, Euclidean distance, Ward’s criterion). (D) Spatial layout of the cell- and gene-clusters identified in (C).

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