title: Study of cell differentiation by phylogenetic analysis using histone modification data.
abstract: BACKGROUND
  In cell differentiation, a cell of a less specialized type becomes one of a more specialized type, even though all cells have the same genome. Transcription factors and epigenetic marks like histone modifications can play a significant role in the differentiation process.
  
  
  RESULTS
  In this paper, we present a simple analysis of cell types and differentiation paths using phylogenetic inference based on ChIP-Seq histone modification data. We precisely defined the notion of cell-type trees and provided a procedure of building such trees. We propose new data representation techniques and distance measures for ChIP-Seq data and use these together with standard phylogenetic inference methods to build biologically meaningful cell-type trees that indicate how diverse types of cells are related. We demonstrate our approach on various kinds of histone modifications for various cell types, also using the datasets to explore various issues surrounding replicate data, variability between cells of the same type, and robustness. We use the results to get some interesting biological findings like important patterns of histone modification changes during cell differentiation process.
  
  
  CONCLUSIONS
  We introduced and studied the novel problem of inferring cell type trees from histone modification data. The promising results we obtain point the way to a new approach to the study of cell differentiation. We also discuss how cell-type trees can be used to study the evolution of cell types.
authors.forename: Nishanth Ulhas
authors.initials: NU
authors.lastname: Nair
authors.forename: Yu
authors.initials: Y
authors.lastname: Lin
authors.forename: Ana
authors.initials: A
authors.lastname: Manasovska
authors.forename: Jelena
authors.initials: J
authors.lastname: Antic
authors.forename: Paulina
authors.initials: P
authors.lastname: Grnarova
authors.forename: Avinash Das
authors.initials: AD
authors.lastname: Sahu
authors.affiliation: School of Computer and Communication Sciences, École Polytechnique Fédérale de Lausanne (EPFL), EPFL IC IIF LCBB, INJ 211 (Batiment INJ), Station 14, CH-1015 Lausanne, Switzerland. philipp.bucher@epfl.ch.
authors.forename: Philipp
authors.initials: P
authors.lastname: Bucher
authors.forename: Bernard M E
authors.initials: BM
authors.lastname: Moret
mesh_terms: D002454:Cell Differentiation / Q000235:genetics*; D047369:Chromatin Immunoprecipitation; D057890:Epigenomics / Q000379:methods*; D006657:Histones / Q000235:genetics / Q000378:metabolism*; D006801:Humans; D010802:Phylogeny; D017422:Sequence Analysis, DNA; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism
chemical_list: D006657:Histones; D014157:Transcription Factors
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