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      Chromas from chromatin: sonification of the epigenome

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      a , 1 , 1 , 1 , 2
      F1000Research
      F1000Research
      Sonification, Chromatin, Music, Information, Epigenomics

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          Abstract

          The epigenetic modifications are organized in patterns determining the functional properties of the underlying genome. Such patterns, typically measured by ChIP-seq assays of histone modifications, can be combined and translated into musical scores, summarizing multiple signals into a single waveform. As music is recognized as a universal way to convey meaningful information, we wanted to investigate properties of music obtained by sonification of ChIP-seq data. We show that the music produced by such quantitative signals is perceived by human listeners as more pleasant than that produced from randomized signals. Moreover, the waveform can be analyzed to predict phenotypic properties, such as differential gene expression.

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          Most cited references12

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          BigWig and BigBed: enabling browsing of large distributed datasets

          Summary: BigWig and BigBed files are compressed binary indexed files containing data at several resolutions that allow the high-performance display of next-generation sequencing experiment results in the UCSC Genome Browser. The visualization is implemented using a multi-layered software approach that takes advantage of specific capabilities of web-based protocols and Linux and UNIX operating systems files, R trees and various indexing and compression tricks. As a result, only the data needed to support the current browser view is transmitted rather than the entire file, enabling fast remote access to large distributed data sets. Availability and implementation: Binaries for the BigWig and BigBed creation and parsing utilities may be downloaded at http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/. Source code for the creation and visualization software is freely available for non-commercial use at http://hgdownload.cse.ucsc.edu/admin/jksrc.zip, implemented in C and supported on Linux. The UCSC Genome Browser is available at http://genome.ucsc.edu Contact: ann@soe.ucsc.edu Supplementary information: Supplementary byte-level details of the BigWig and BigBed file formats are available at Bioinformatics online. For an in-depth description of UCSC data file formats and custom tracks, see http://genome.ucsc.edu/FAQ/FAQformat.html and http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html
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            Charting histone modifications and the functional organization of mammalian genomes.

            A succession of technological advances over the past decade have enabled researchers to chart maps of histone modifications and related chromatin structures with increasing accuracy, comprehensiveness and throughput. The resulting data sets highlight the interplay between chromatin and genome function, dynamic variations in chromatin structure across cellular conditions, and emerging roles for large-scale domains and higher-ordered chromatin organization. Here we review a selection of recent studies that have probed histone modifications and successive layers of chromatin structure in mammalian genomes, the patterns that have been identified and future directions for research.
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              Integrative annotation of chromatin elements from ENCODE data

              The ENCODE Project has generated a wealth of experimental information mapping diverse chromatin properties in several human cell lines. Although each such data track is independently informative toward the annotation of regulatory elements, their interrelations contain much richer information for the systematic annotation of regulatory elements. To uncover these interrelations and to generate an interpretable summary of the massive datasets of the ENCODE Project, we apply unsupervised learning methodologies, converting dozens of chromatin datasets into discrete annotation maps of regulatory regions and other chromatin elements across the human genome. These methods rediscover and summarize diverse aspects of chromatin architecture, elucidate the interplay between chromatin activity and RNA transcription, and reveal that a large proportion of the genome lies in a quiescent state, even across multiple cell types. The resulting annotation of non-coding regulatory elements correlate strongly with mammalian evolutionary constraint, and provide an unbiased approach for evaluating metrics of evolutionary constraint in human. Lastly, we use the regulatory annotations to revisit previously uncharacterized disease-associated loci, resulting in focused, testable hypotheses through the lens of the chromatin landscape.
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                Author and article information

                Journal
                F1000Res
                F1000Res
                F1000Research
                F1000Research
                F1000Research (London, UK )
                2046-1402
                3 March 2016
                2016
                : 5
                : 274
                Affiliations
                [1 ]Center for Translational Genomics and Bioinformatics, San Raffaele Hospital- via olgettina 58, 20138 Milano, Italy
                [2 ]Department of Molecular Biotechnology and Life Sciences, University of Turin - via Nizza 52, 10126 Torino, Italy
                [1 ]Department of Systems Biology, Columbia University, New York, NY, USA
                [1 ]Otto-Warburg-Laboratory, Max Planck Institute for Molecular Genetics, Berlin, Germany
                [1 ]Department of Biochemistry, University at Buffalo, Buffalo, NY, USA
                [2 ]Department of Biostatistics, University at Buffalo, Buffalo, NY, USA
                Author notes

                DC, DL and PP designed the experiment and wrote the manuscript; DC performed the analysis.

                Competing interests: No competing interests were disclosed.

                Competing interests: No competing interests were disclosed.

                Competing interests: No competing interests were disclosed.

                Competing interests: No competing interests were disclosed.

                Article
                10.12688/f1000research.8001.1
                4805159
                27019695
                69cc4d50-70d3-4735-ae8a-aa46a12e7a6f
                Copyright: © 2016 Cittaro D et al.

                This is an open access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                : 17 February 2016
                Funding
                The author(s) declared that no grants were involved in supporting this work.
                Categories
                Research Article
                Articles
                Genomics

                sonification,chromatin,music,information,epigenomics
                sonification, chromatin, music, information, epigenomics

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