publication . Article . 2016

Chromas from chromatin: sonification of the epigenome

Davide Cittaro; Dejan Lazarevic; Paolo Provero;
  • Published: 01 Mar 2016
  • Publisher: F1000 Research, Ltd.
Abstract
<ns4:p>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 ...
Subjects
Medical Subject Headings: humanitiesbehavioral disciplines and activitieshuman activities
free text keywords: Epigenome, Epigenomics, Open science, Chromatin, Epigenetics, Computational biology, Open peer review, Plant biology, Neuroscience, Sonification, Biology, Research Article, Articles, Genomics, Music, Information
Communities
Digital Humanities and Cultural Heritage
32 references, page 1 of 3

1 Ohno S Ohno M: The all pervasive principle of repetitious recurrence governs not only coding sequence construction but also human endeavor in musical composition.Immunogenetics.1986;24(2):71–78. 10.1007/BF00373112 3744439 [PubMed] [DOI]

2 King RD Angus CG: PM--protein music.Comput Appl Biosci.1996;12(3):251–252. 10.1093/bioinformatics/12.3.251 8872396 [OpenAIRE] [PubMed] [DOI]

3 Takahashi R Miller JH: Conversion of amino-acid sequence in proteins to classical music: search for auditory patterns.Genome Biol.2007;8(5):405. 10.1186/gb-2007-8-5-405 17477882 [OpenAIRE] [PubMed] [DOI]

4 Larsen P Gilbert J: Microbial bebop: creating music from complex dynamics in microbial ecology.PLoS One.2013;8(3):e58119. 10.1371/journal.pone.0058119 23483981 [OpenAIRE] [PubMed] [DOI]

5 Juslin PN: What does music express? Basic emotions and beyond.Front Psychol.2013;4:596. 10.3389/fpsyg.2013.00596 24046758 [OpenAIRE] [PubMed] [DOI]

6 1000 Genomes Project Consortium, Abecasis GR Auton A: An integrated map of genetic variation from 1,092 human genomes.Nature.2012;491(7422):56–65. 10.1038/nature11632 23128226 [OpenAIRE] [PubMed] [DOI]

7 Zhang Y Liu T Meyer CA: Model-based analysis of ChIP-Seq (MACS).Genome Biol.2008;9(9):R137. 10.1186/gb-2008-9-9-r137 18798982 [OpenAIRE] [PubMed] [DOI]

8 Robinson MD McCarthy DJ Smyth GK: edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics.2010;26(1):139–40. 10.1093/bioinformatics/btp616 19910308 [OpenAIRE] [PubMed] [DOI]

9 Kouzarides T: Chromatin modifications and their function.Cell.2007;128(4):693–705. 10.1016/j.cell.2007.02.005 17320507 [OpenAIRE] [PubMed] [DOI]

10 ENCODE Project Consortium: An integrated encyclopedia of DNA elements in the human genome.Nature.2012;489(7414):57–74. 10.1038/nature11247 22955616 [OpenAIRE] [PubMed] [DOI]

11 SEQC/MAQC-III Consortium: A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium.Nat Biotechnol.2014;32(9):903–14. 10.1038/nbt.2957 25150838 [OpenAIRE] [PubMed] [DOI]

12 Logan B: Mel Frequency Cepstral Coefficients for Music Modeling.ISMIR.2000 Reference Source

13 Dopler M Schedl M Pohle T: Accessing Music Collections Via Representative Cluster Prototypes in a Hierarchical Organization Scheme.ISMIR.2008 Reference Source [OpenAIRE]

14 Aucouturier JJ Pachet F Sandler M: “The way it Sounds”: timbre models for analysis and retrieval of music signals.IEEE Trans Multimedia.2005;7(6):1028–1035. 10.1109/TMM.2005.858380 [OpenAIRE] [DOI]

15 Zhou VW Goren A Bernstein BE: Charting histone modifications and the functional organization of mammalian genomes.Nat Rev Genet.2011;12(1):7–18. 10.1038/nrg2905 21116306 [OpenAIRE] [PubMed] [DOI]

32 references, page 1 of 3
Abstract
<ns4:p>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 ...
Subjects
Medical Subject Headings: humanitiesbehavioral disciplines and activitieshuman activities
free text keywords: Epigenome, Epigenomics, Open science, Chromatin, Epigenetics, Computational biology, Open peer review, Plant biology, Neuroscience, Sonification, Biology, Research Article, Articles, Genomics, Music, Information
Communities
Digital Humanities and Cultural Heritage
32 references, page 1 of 3

1 Ohno S Ohno M: The all pervasive principle of repetitious recurrence governs not only coding sequence construction but also human endeavor in musical composition.Immunogenetics.1986;24(2):71–78. 10.1007/BF00373112 3744439 [PubMed] [DOI]

2 King RD Angus CG: PM--protein music.Comput Appl Biosci.1996;12(3):251–252. 10.1093/bioinformatics/12.3.251 8872396 [OpenAIRE] [PubMed] [DOI]

3 Takahashi R Miller JH: Conversion of amino-acid sequence in proteins to classical music: search for auditory patterns.Genome Biol.2007;8(5):405. 10.1186/gb-2007-8-5-405 17477882 [OpenAIRE] [PubMed] [DOI]

4 Larsen P Gilbert J: Microbial bebop: creating music from complex dynamics in microbial ecology.PLoS One.2013;8(3):e58119. 10.1371/journal.pone.0058119 23483981 [OpenAIRE] [PubMed] [DOI]

5 Juslin PN: What does music express? Basic emotions and beyond.Front Psychol.2013;4:596. 10.3389/fpsyg.2013.00596 24046758 [OpenAIRE] [PubMed] [DOI]

6 1000 Genomes Project Consortium, Abecasis GR Auton A: An integrated map of genetic variation from 1,092 human genomes.Nature.2012;491(7422):56–65. 10.1038/nature11632 23128226 [OpenAIRE] [PubMed] [DOI]

7 Zhang Y Liu T Meyer CA: Model-based analysis of ChIP-Seq (MACS).Genome Biol.2008;9(9):R137. 10.1186/gb-2008-9-9-r137 18798982 [OpenAIRE] [PubMed] [DOI]

8 Robinson MD McCarthy DJ Smyth GK: edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics.2010;26(1):139–40. 10.1093/bioinformatics/btp616 19910308 [OpenAIRE] [PubMed] [DOI]

9 Kouzarides T: Chromatin modifications and their function.Cell.2007;128(4):693–705. 10.1016/j.cell.2007.02.005 17320507 [OpenAIRE] [PubMed] [DOI]

10 ENCODE Project Consortium: An integrated encyclopedia of DNA elements in the human genome.Nature.2012;489(7414):57–74. 10.1038/nature11247 22955616 [OpenAIRE] [PubMed] [DOI]

11 SEQC/MAQC-III Consortium: A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium.Nat Biotechnol.2014;32(9):903–14. 10.1038/nbt.2957 25150838 [OpenAIRE] [PubMed] [DOI]

12 Logan B: Mel Frequency Cepstral Coefficients for Music Modeling.ISMIR.2000 Reference Source

13 Dopler M Schedl M Pohle T: Accessing Music Collections Via Representative Cluster Prototypes in a Hierarchical Organization Scheme.ISMIR.2008 Reference Source [OpenAIRE]

14 Aucouturier JJ Pachet F Sandler M: “The way it Sounds”: timbre models for analysis and retrieval of music signals.IEEE Trans Multimedia.2005;7(6):1028–1035. 10.1109/TMM.2005.858380 [OpenAIRE] [DOI]

15 Zhou VW Goren A Bernstein BE: Charting histone modifications and the functional organization of mammalian genomes.Nat Rev Genet.2011;12(1):7–18. 10.1038/nrg2905 21116306 [OpenAIRE] [PubMed] [DOI]

32 references, page 1 of 3
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publication . Article . 2016

Chromas from chromatin: sonification of the epigenome

Davide Cittaro; Dejan Lazarevic; Paolo Provero;