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Cell cycle expression heterogeneity predicts degree of differentiation.

ABSTRACT: Methods that predict fate potential or degree of differentiation from transcriptomic data have identified rare progenitor populations and uncovered developmental regulatory mechanisms. However, some state-of-the-art methods are too computationally burdensome for emerging large-scale data and all methods make inaccurate predictions in certain biological systems. We developed a method in R (stemFinder) that predicts single cell differentiation time based on heterogeneity in cell cycle gene expression. Our method is computationally tractable and is as good as or superior to competitors. As part of our benchmarking, we implemented four different performance metrics to assist potential users in selecting the tool that is most apt for their application. Finally, we explore the relationship between differentiation time and cell fate potential by analyzing a lineage tracing dataset with clonally labelled hematopoietic cells, revealing that metrics of differentiation time are correlated with the number of downstream lineages.

SUBMITTER: Noller K

PROVIDER: S-EPMC11291076 | biostudies-literature | 2024 Jul

REPOSITORIES: biostudies-literature

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Cell cycle expression heterogeneity predicts degree of differentiation.

Noller Kathleen K Cahan Patrick P

bioRxiv : the preprint server for biology 20240722

Methods that predict fate potential or degree of differentiation from transcriptomic data have identified rare progenitor populations and uncovered developmental regulatory mechanisms. However, some state-of-the-art methods are too computationally burdensome for emerging large-scale data and all methods make inaccurate predictions in certain biological systems. We developed a method in R (stemFinder) that predicts single cell differentiation time based on heterogeneity in cell cycle gene express ...[more]

PMID: 39091773

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Cell cycle expression heterogeneity predicts degree of differentiation.

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