Tree-Based Co-Clustering Identifies Chromatin Accessibility Patterns Associated With Hematopoietic Lineage Structure.

ABSTRACT: Chromatin accessibility, as measured by ATACseq, varies between hematopoietic cell types in different lineages of the hematopoietic differentiation tree, e.g. T cells vs. B cells, but methods that associate variation in chromatin accessibility to the lineage structure of the differentiation tree are lacking. Using an ATACseq dataset recently published by the ImmGen consortium, we construct associations between chromatin accessibility and hematopoietic cell types using a novel co-clustering approach that accounts for the structure of the hematopoietic, differentiation tree. Under a model in which all loci and cell types within a co-cluster have a shared accessibility state, we show that roughly 80% of cell type associated accessibility variation can be captured through 12 cell type clusters

SUBMITTER: George TB 

PROVIDER: S-EPMC8517275 | biostudies-literature | 2021

REPOSITORIES: biostudies-literature