Quartet-based inference of cell differentiation trees from ChIP-Seq histone modification data

Nazifa Ahmed Moumi, Badhan Das, Zarin Tasnim Promi, Nishat Anjum Bristy and Md Shamsuzzoha Bayzid

PLOS ONE, 2019, vol. 14, issue 9, 1-25

Abstract: Understanding cell differentiation—the process of generation of distinct cell-types—plays a pivotal role in developmental and evolutionary biology. Transcriptomic information and epigenetic marks are useful to elucidate hierarchical developmental relationships among cell-types. Standard phylogenetic approaches such as maximum parsimony, maximum likelihood and neighbor joining have previously been applied to ChIP-Seq histone modification data to infer cell-type trees, showing how diverse types of cells are related. In this study, we demonstrate the applicability and suitability of quartet-based phylogenetic tree estimation techniques for constructing cell-type trees. We propose two quartet-based pipelines for constructing cell phylogeny. Our methods were assessed for their validity in inferring hierarchical differentiation processes of various cell-types in H3K4me3, H3K27me3, H3K36me3, and H3K27ac histone mark data. We also propose a robust metric for evaluating cell-type trees.

Date: 2019
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Persistent link: https://EconPapers.repec.org/RePEc:plo:pone00:0221270

DOI: 10.1371/journal.pone.0221270

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