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Fig. 3 | BMC Bioinformatics

Fig. 3

From: eSPRESSO: topological clustering of single-cell transcriptomics data to reveal informative genes for spatio–temporal architectures of cells

Fig. 3

Virtual knockout (VKO) analysis for mouse developmental heart in eSPRESSO. a Graph representation of topology of cells or tissues and a topological distance map of cells for the original (lower left) and resultant (upper right) clusters. b 3D reconstruction of cells with SDGs using UMAP. c Gene expression heatmap for the optimized SDGs. d GO mapping of SDGs in Biological Process. The p-values determined by hypergeometric distribution statistics are shown on top of bars. e–g 3D reconstruction of cells with VKO analysis by e single gene KO: Des– (left), Ptma– (center), or Ccnd2– (right); f double gene KO: Des–Ptma–; and g triple gene KO: Des–Ptma–Ccnd2–. h Gene expression gradients in reconstructed 3D structure for VKO genes

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BMC Bioinformatics

ISSN: 1471-2105

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