2012
DOI: 10.1038/nmeth.1937
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Unsupervised pattern discovery in human chromatin structure through genomic segmentation

Abstract: We applied a dynamic Bayesian network method that identifies joint patterns from multiple functional genomics experiments to ChIP-seq histone modification and transcription factor data, and DNaseI-seq and FAIRE-seq open chromatin readouts from the human cell line K562. In an unsupervised fashion, we identified patterns associated with transcription start sites, gene ends, enhancers, CTCF elements, and repressed regions. Software and genome browser tracks are at http://noble.gs.washington.edu/proj/segway/.

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Cited by 573 publications
(534 citation statements)
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“…Book-ended bins that have the same state are merged. The output of this process is genome segmentation into variable-width non-overlapping chromatin states similar to Segway (Hoffman et al, 2012) and ChromHMM (Ernst and Kellis, 2012). …”
Section: Methodsmentioning
confidence: 99%
“…Book-ended bins that have the same state are merged. The output of this process is genome segmentation into variable-width non-overlapping chromatin states similar to Segway (Hoffman et al, 2012) and ChromHMM (Ernst and Kellis, 2012). …”
Section: Methodsmentioning
confidence: 99%
“…Combinations of histone modifications are often observed together in chromatin states, patterns indicative of distinct modes of biological activity. These patterns may be identified by integrating multiple histone modification ChIP-seq data sets using the ChromHMM 97 or SegWay 98 algorithms.…”
Section: Analytical Techniques For Bias Correctionmentioning
confidence: 99%
“…Large-scale, systematic efforts to perform ChIP with carefully validated antibodies in multiple cell lines have generated an invaluable resource for the genomics community [43,44]. Histone modification ChIP data are useful for both identification of regulatory elements [45] more generally as an input to computational strategies for determining chromatin states [46,47]. TF ChIP data sets have been fed into TF binding motif databases [4850] and combined with open chromatin data to create genome-wide maps of presumptive TF binding in cell lines where individual TF ChIP experiments were not necessarily performed [8,30].…”
Section: Primary Structurementioning
confidence: 99%