000202426 001__ 202426
000202426 005__ 20181203023632.0
000202426 0247_ $$2doi$$a10.1186/1471-2105-15-269
000202426 022__ $$a1471-2105
000202426 02470 $$2ISI$$a000340800200001
000202426 037__ $$aARTICLE
000202426 245__ $$aStudy of cell differentiation by phylogenetic analysis using histone modification data
000202426 260__ $$aLondon$$bBioMed Central$$c2014
000202426 269__ $$a2014
000202426 300__ $$a15
000202426 336__ $$aJournal Articles
000202426 520__ $$aBackground: 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.
000202426 6531_ $$aCell differentiation
000202426 6531_ $$aDevelopment
000202426 6531_ $$aCell-type trees
000202426 6531_ $$aEpigenomics
000202426 6531_ $$aHistone modifications
000202426 6531_ $$aPhylogenetics
000202426 6531_ $$aEvolution of cell types
000202426 700__ $$aNair, Nishanth Ulhas$$uEcole Polytech Fed Lausanne, EPFL IC IIF LCBB, Sch Comp & Commun Sci, CH-1015 Lausanne, Switzerland
000202426 700__ $$0240032$$aLin, Yu$$g176808$$uUniv Calif San Diego, Dept Comp Sci & Engn, San Diego, CA 92103 USA
000202426 700__ $$aManasovska, Ana$$uEcole Polytech Fed Lausanne, EPFL IC IIF LCBB, Sch Comp & Commun Sci, CH-1015 Lausanne, Switzerland
000202426 700__ $$aAntic, Jelena$$uEcole Polytech Fed Lausanne, EPFL IC IIF LCBB, Sch Comp & Commun Sci, CH-1015 Lausanne, Switzerland
000202426 700__ $$aGrnarova, Paulina$$uEcole Polytech Fed Lausanne, EPFL IC IIF LCBB, Sch Comp & Commun Sci, CH-1015 Lausanne, Switzerland
000202426 700__ $$aDas Sahu, Avinash$$uUniv Maryland, Dept Comp Sci, College Pk, MD 20742 USA
000202426 700__ $$0244404$$aBucher, Philipp$$g113607$$uEcole Polytech Fed Lausanne, Sch Life Sci, Lausanne, Switzerland
000202426 700__ $$0241987$$aMoret, Bernard M. E.$$g172233$$uEcole Polytech Fed Lausanne, EPFL IC IIF LCBB, Sch Comp & Commun Sci, CH-1015 Lausanne, Switzerland
000202426 773__ $$j15$$k269$$tBmc Bioinformatics
000202426 909C0 $$0252020$$pLCBB$$xU11274
000202426 909C0 $$0252244$$pGR-BUCHER$$xU11780
000202426 909CO $$ooai:infoscience.tind.io:202426$$pSV$$pIC$$particle
000202426 917Z8 $$x172233
000202426 937__ $$aEPFL-ARTICLE-202426
000202426 973__ $$aEPFL$$rREVIEWED$$sPUBLISHED
000202426 980__ $$aARTICLE