A Short Report on the Markov Property of DNA Sequences on 200-bp Genomic Units of Roadmap Genomics ChromHMM Annotations: A Computational Perspective
The non-coding DNA in eukaryotic genomes encodes a language that programs chromatin accessibility, transcription factor binding, and various other activities. The objective of this study was to determine the effect of the primary DNA sequence on the epigenomic landscape across a 200-base pair of gen...
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| Format: | Article |
| Language: | English |
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Korea Genome Organization
2018-12-01
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| Series: | Genomics & Informatics |
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| Online Access: | http://genominfo.org/upload/pdf/gi-2018-16-4-e27.pdf |
| _version_ | 1819232016325935104 |
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| author | Hyun-Seok Park |
| author_facet | Hyun-Seok Park |
| author_sort | Hyun-Seok Park |
| collection | DOAJ |
| description | The non-coding DNA in eukaryotic genomes encodes a language that programs chromatin accessibility, transcription factor binding, and various other activities. The objective of this study was to determine the effect of the primary DNA sequence on the epigenomic landscape across a 200-base pair of genomic units by integrating 127 publicly available ChromHMM BED files from the Roadmap Genomics project. Nucleotide frequency profiles of 127 chromatin annotations stratified by chromatin variability were analyzed and integrative hidden Markov models were built to detect Markov properties of chromatin regions. Our aim was to identify the relationship between DNA sequence units and their chromatin variability based on integrated ChromHMM datasets of different cell and tissue types. |
| first_indexed | 2024-12-23T11:54:09Z |
| format | Article |
| id | doaj.art-db0dbf2b93cf48e295a528efdcbdb164 |
| institution | Directory Open Access Journal |
| issn | 2234-0742 |
| language | English |
| last_indexed | 2024-12-23T11:54:09Z |
| publishDate | 2018-12-01 |
| publisher | Korea Genome Organization |
| record_format | Article |
| series | Genomics & Informatics |
| spelling | doaj.art-db0dbf2b93cf48e295a528efdcbdb1642022-12-21T17:48:07ZengKorea Genome OrganizationGenomics & Informatics2234-07422018-12-0116410.5808/GI.2018.16.4.e27529A Short Report on the Markov Property of DNA Sequences on 200-bp Genomic Units of Roadmap Genomics ChromHMM Annotations: A Computational PerspectiveHyun-Seok Park0 Bioinformatics Laboratory, ELTEC College of Engineering, Ewha Womans University, Seoul 03760, KoreaThe non-coding DNA in eukaryotic genomes encodes a language that programs chromatin accessibility, transcription factor binding, and various other activities. The objective of this study was to determine the effect of the primary DNA sequence on the epigenomic landscape across a 200-base pair of genomic units by integrating 127 publicly available ChromHMM BED files from the Roadmap Genomics project. Nucleotide frequency profiles of 127 chromatin annotations stratified by chromatin variability were analyzed and integrative hidden Markov models were built to detect Markov properties of chromatin regions. Our aim was to identify the relationship between DNA sequence units and their chromatin variability based on integrated ChromHMM datasets of different cell and tissue types.http://genominfo.org/upload/pdf/gi-2018-16-4-e27.pdfchromatin mapscomputational epigeneticsMarkov chainnoncoding DNAnucleotide frequency patterns |
| spellingShingle | Hyun-Seok Park A Short Report on the Markov Property of DNA Sequences on 200-bp Genomic Units of Roadmap Genomics ChromHMM Annotations: A Computational Perspective Genomics & Informatics chromatin maps computational epigenetics Markov chain noncoding DNA nucleotide frequency patterns |
| title | A Short Report on the Markov Property of DNA Sequences on 200-bp Genomic Units of Roadmap Genomics ChromHMM Annotations: A Computational Perspective |
| title_full | A Short Report on the Markov Property of DNA Sequences on 200-bp Genomic Units of Roadmap Genomics ChromHMM Annotations: A Computational Perspective |
| title_fullStr | A Short Report on the Markov Property of DNA Sequences on 200-bp Genomic Units of Roadmap Genomics ChromHMM Annotations: A Computational Perspective |
| title_full_unstemmed | A Short Report on the Markov Property of DNA Sequences on 200-bp Genomic Units of Roadmap Genomics ChromHMM Annotations: A Computational Perspective |
| title_short | A Short Report on the Markov Property of DNA Sequences on 200-bp Genomic Units of Roadmap Genomics ChromHMM Annotations: A Computational Perspective |
| title_sort | short report on the markov property of dna sequences on 200 bp genomic units of roadmap genomics chromhmm annotations a computational perspective |
| topic | chromatin maps computational epigenetics Markov chain noncoding DNA nucleotide frequency patterns |
| url | http://genominfo.org/upload/pdf/gi-2018-16-4-e27.pdf |
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