scGOclust

scGOclust leverages Gene Ontology (GO) terms to compare cell type functional profiles across and within species, even when phylogenetically distant, facilitating the discovery of functionally analogous cell types by constructing de novo cellular functional profiles.

Key Features:

• Cross-species comparison: Enables systematic and robust comparisons of cell type functional profiles within and across phylogenetically distant species using GO terms.
• De novo functional profiling: Constructs cellular functional profiles de novo from GO terms rather than relying on direct gene orthology.
• Functional spectrum recapitulation: Effectively recapitulates the function spectrum of different cell types from single-cell data.
• Functional similarity characterization: Characterizes functional similarities between homologous cell types and reveals functional convergence between unrelated cell types.

Scientific Applications:

• Comparative analysis of heart, gut, and kidney: Applied to analyse and compare these organs between mouse and fly.
• Whole-body cross-species comparison: Applied to compare whole-body data from Caenorhabditis elegans and Hydra vulgaris.
• Subpopulation identification: Identified subpopulations within the fly crop that show circadian rhythm-regulated secretory properties.
• Cell type analogy hypothesis generation: Hypothesized an analogy between fly principal cells from different segments and distinct mouse kidney tubules.
• Evolutionary and functional biology: Uncovers functionally analogous cell types or organs across distant species, offering perspectives on evolutionary and functional biology.

Methodology:

scGOclust constructs de novo cellular functional profiles using GO terms. The method uses the gene ontology (GO) knowledgebase as a comprehensive resource of gene functions across species, providing a bridge for distant species comparisons when gene-based comparisons become less informative due to phylogenetic distance.