Open AccessQuartet-based inference of cell differentiation trees from ChIP-Seq histone modification data
Author(s) -
Nazifa Ahmed Moumi,
Badhan Das,
Zarin Tasnim Promi,
Nishat Anjum Bristy,
Md. Shamsuzzoha Bayzid
Publication year - 2019
Publication title -
plos one
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.99
H-Index - 332
ISSN - 1932-6203
DOI - 10.1371/journal.pone.0221270
Subject(s) - h3k4me3 , phylogenetic tree , histone , biology , computational biology , inference , cell type , epigenetics , phylogenetics , cellular differentiation , tree (set theory) , computer science , evolutionary biology , genetics , gene , cell , artificial intelligence , gene expression , mathematics , mathematical analysis , promoter
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.