Quartet-based inference of cell differentiation trees from ChIP-Seq histone modification data
Autoři:
Nazifa Ahmed Moumi aff001; Badhan Das aff001; Zarin Tasnim Promi aff001; Nishat Anjum Bristy aff001; Md. Shamsuzzoha Bayzid aff001
Působiště autorů:
Department of Computer Science and Engineering, Bangladesh University of Engineering and Technology, Dhaka, Bangladesh
aff001
Vyšlo v časopise:
PLoS ONE 14(9)
Kategorie:
Research Article
prolekare.web.journal.doi_sk:
https://doi.org/10.1371/journal.pone.0221270
Souhrn
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.
Klíčová slova:
Principal component analysis – Epigenetics – Phylogenetics – Phylogenetic analysis – Cell differentiation – Blood – Fibroblasts – Lung development
Zdroje
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