A Short Report on the Markov Property of DNA Sequences on 200-bp Genomic Units of ENCODE/Broad ChromHMM Annotations: A Computational Perspective
The non-coding DNA in eukaryotic genomes encodes a language which programs chromatin accessibility, transcription factor binding, and various other activities. The objective of this short report was to determine the impact of primary DNA sequence on the epigenomic landscape across 200-base pair geno...
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BioMed Central
2018-09-01
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| Series: | Genomics & Informatics |
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| Online Access: | http://genominfo.org/upload/pdf/gi-2018-16-3-65.pdf |
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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 which programs chromatin accessibility, transcription factor binding, and various other activities. The objective of this short report was to determine the impact of primary DNA sequence on the epigenomic landscape across 200-base pair genomic units by integrating nine publicly available ChromHMM Browser Extensible Data files of the Encyclopedia of DNA Elements (ENCODE) project. The nucleotide frequency profiles of nine chromatin annotations with the units of 200 bp were analyzed and integrative Markov chains were built to detect the Markov properties of the DNA sequences in some of the active chromatin states of different ChromHMM regions. Our aim was to identify the possible relationship between DNA sequences and the newly built chromatin states based on the integrated ChromHMM datasets of different cells and tissue types. |
| format | Article |
| id | doaj-art-c921462389404e27a3b02497fea6bd1c |
| institution | Kabale University |
| issn | 2234-0742 |
| language | English |
| publishDate | 2018-09-01 |
| publisher | BioMed Central |
| record_format | Article |
| series | Genomics & Informatics |
| spelling | doaj-art-c921462389404e27a3b02497fea6bd1c2025-02-02T23:39:17ZengBioMed CentralGenomics & Informatics2234-07422018-09-01163657010.5808/GI.2018.16.3.65515A Short Report on the Markov Property of DNA Sequences on 200-bp Genomic Units of ENCODE/Broad 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 which programs chromatin accessibility, transcription factor binding, and various other activities. The objective of this short report was to determine the impact of primary DNA sequence on the epigenomic landscape across 200-base pair genomic units by integrating nine publicly available ChromHMM Browser Extensible Data files of the Encyclopedia of DNA Elements (ENCODE) project. The nucleotide frequency profiles of nine chromatin annotations with the units of 200 bp were analyzed and integrative Markov chains were built to detect the Markov properties of the DNA sequences in some of the active chromatin states of different ChromHMM regions. Our aim was to identify the possible relationship between DNA sequences and the newly built chromatin states based on the integrated ChromHMM datasets of different cells and tissue types.http://genominfo.org/upload/pdf/gi-2018-16-3-65.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 ENCODE/Broad 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 ENCODE/Broad ChromHMM Annotations: A Computational Perspective |
| title_full | A Short Report on the Markov Property of DNA Sequences on 200-bp Genomic Units of ENCODE/Broad ChromHMM Annotations: A Computational Perspective |
| title_fullStr | A Short Report on the Markov Property of DNA Sequences on 200-bp Genomic Units of ENCODE/Broad ChromHMM Annotations: A Computational Perspective |
| title_full_unstemmed | A Short Report on the Markov Property of DNA Sequences on 200-bp Genomic Units of ENCODE/Broad ChromHMM Annotations: A Computational Perspective |
| title_short | A Short Report on the Markov Property of DNA Sequences on 200-bp Genomic Units of ENCODE/Broad ChromHMM Annotations: A Computational Perspective |
| title_sort | short report on the markov property of dna sequences on 200 bp genomic units of encode broad chromhmm annotations a computational perspective |
| topic | chromatin maps computational epigenetics Markov chain noncoding DNA nucleotide frequency patterns |
| url | http://genominfo.org/upload/pdf/gi-2018-16-3-65.pdf |
| work_keys_str_mv | AT hyunseokpark ashortreportonthemarkovpropertyofdnasequenceson200bpgenomicunitsofencodebroadchromhmmannotationsacomputationalperspective AT hyunseokpark shortreportonthemarkovpropertyofdnasequenceson200bpgenomicunitsofencodebroadchromhmmannotationsacomputationalperspective |