plantScGRN:

A reference single-cell transcriptomic atlas of Arabidopsis seedlings

Integration of 63 published scRNA-seq datasets illuminates the regulatory network architecture of plant cell fate specification.
Toptargets

Comprehensive integration analysis

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Cell-type Specific Gene Regulatory Networks

We constructed gene regulatory networks (GRNs) consisting of both the regulons and their target genes with tissue-specific gene expression. In total, we identified 638 regulons across all types of cells.

Gene Expression Pattern in Each Celltype

To generate a reference single-cell transcriptomic atlas of the whole Arabidopsis seedling and thus to reconstruct the cellular taxonomy across the plant body, we performed comprehensive integration analysis of single-cell RNA sequencing (scRNA-seq) data generated from representative tissues in Arabidopsis juvenile seedlings.

Functional Annotation of Atlas

In order to identify cell-type specific gene expression programs (GEPs) with biological meanings, we used the CellFunTopic framework to infer enriched biological pathways for DEGs among different cell types.

Top regulons of each celltype


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Bubble Plot

Violin Plot

GSEA result



Heatmap

PathwayScatterplot

edge_bundling_GSEA


Hierarchyplot


Topic modeling network




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