000183820 001__ 183820
000183820 005__ 20190316235551.0
000183820 0247_ $$2doi$$a10.1371/journal.pone.0039573
000183820 022__ $$a1932-6203
000183820 02470 $$2ISI$$a000307284100003
000183820 037__ $$aARTICLE
000183820 245__ $$aChIPnorm: a statistical method for normalizing and identifying differential regions in histone modification ChIP-seq libraries
000183820 269__ $$a2012
000183820 260__ $$bPublic Library of Science$$c2012$$aSan Francisco
000183820 300__ $$a14
000183820 336__ $$aJournal Articles
000183820 520__ $$aThe advent of high-throughput technologies such as ChIP-seq has made possible the study of histone modifications. A problem of particular interest is the identification of regions of the genome where different cell types from the same organism exhibit different patterns of histone enrichment. This problem turns out to be surprisingly difficult, even in simple pairwise comparisons, because of the significant level of noise in ChIP-seq data. In this paper we propose a two-stage statistical method, called ChIPnorm, to normalize ChIP-seq data, and to find differential regions in the genome, given two libraries of histone modifications of different cell types. We show that the ChIPnorm method removes most of the noise and bias in the data and outperforms other normalization methods. We correlate the histone marks with gene expression data and confirm that histone modifications H3K27me3 and H3K4me3 act as respectively a repressor and an activator of genes. Compared to what was previously reported in the literature, we find that a substantially higher fraction of bivalent marks in ES cells for H3K27me3 and H3K4me3 move into a K27-only state. We find that most of the promoter regions in protein-coding genes have differential histone-modification sites. The software for this work can be downloaded from http://lcbb.epfl.ch/software.html.
000183820 700__ $$0242195$$g190820$$aNair, Nishanth
000183820 700__ $$aDas Sahu, Avinash
000183820 700__ $$0244404$$g113607$$aBucher, Philipp
000183820 700__ $$g172233$$0241987$$aMoret, Bernard
000183820 773__ $$j7$$tPlos One$$k8$$qe39573
000183820 8564_ $$uhttps://infoscience.epfl.ch/record/183820/files/journal.pone.0039573.pdf$$zPublisher's version$$s703289$$yPublisher's version
000183820 909C0 $$xU11274$$0252020$$pLCBB
000183820 909C0 $$0252244$$pGR-BUCHER$$xU11780
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000183820 917Z8 $$x190564
000183820 917Z8 $$x182396
000183820 937__ $$aEPFL-ARTICLE-183820
000183820 973__ $$rREVIEWED$$sPUBLISHED$$aEPFL
000183820 980__ $$aARTICLE