Combinatorial expression motifs in signaling pathways

Cell Genom. 2024 Jan 10;4(1):100463. doi: 10.1016/j.xgen.2023.100463.


In animal cells, molecular pathways often comprise families of variant components, such as ligands or receptors. These pathway components are differentially expressed by different cell types, potentially tailoring pathway function to cell context. However, it has remained unclear how pathway expression profiles are distributed across cell types and whether similar profiles can occur in dissimilar cell types. Here, using single-cell gene expression datasets, we identified pathway expression motifs, defined as recurrent expression profiles that are broadly distributed across diverse cell types. Motifs appeared in core pathways, including TGF-β, Notch, Wnt, and the SRSF splice factors, and involved combinatorial co-expression of multiple components. Motif usage was weakly correlated between pathways in adult cell types and during dynamic developmental transitions. Together, these results suggest a mosaic view of cell type organization, in which different cell types operate many of the same pathways in distinct modes.

Keywords: cell atlas; developmental signaling; integrated data; motifs; signaling pathways; signaling receptors; single cell; transcriptional profiles; transcriptome.

MeSH terms

  • Animals
  • Signal Transduction* / genetics
  • Transforming Growth Factor beta* / genetics


  • Transforming Growth Factor beta