ArticleNucleic acids research2013
Discovery of cell-type specific regulatory elements in the human genome using differential chromatin modification analysis.
Article in Nucleic acids research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed, 20 citations in OpenAlex.
- Anomaly detection in genomic catalogues using unsupervised multi-view autoencoders.BMC bioinformatics · 2021Article
- Joint reconstruction of cis-regulatory interaction networks across multiple tissues using single-cell chromatin accessibility data.Briefings in bioinformatics · 2021Article
- Cis-Regulatory Code for Predicting Plant Cell-Type Transcriptional Response to High Salinity.Plant physiology · 2019Article
- Genome-wide analysis of epigenetic dynamics across human developmental stages and tissues.BMC genomics · 2019Article
- Making Sense of the Epigenome Using Data Integration Approaches.Frontiers in pharmacology · 2019Review
- Reveal cell type-specific regulatory elements and their characterized histone code classes via a hidden Markov model.BMC genomics · 2018Article
- Modeling the relationship of epigenetic modifications to transcription factor binding.Nucleic acids research · 2015Article
- Computational and experimental methods to decipher the epigenetic code.Frontiers in genetics · 2014Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
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Abstract
Chromatin modifications have been comprehensively illustrated to play important roles in gene regulation and cell diversity in recent years. Given the rapid accumulation of genome-wide chromatin modification maps across multiple cell types, there is an urgent need for computational methods to analyze multiple maps to reveal combinatorial modification patterns and define functional DNA elements, especially those are specific to cell types or tissues. In this current study, we developed a computational method using differential chromatin modification analysis (dCMA) to identify cell-type-specific genomic regions with distinctive chromatin modifications. We then apply this method to a public data set with modification profiles of nine marks for nine cell types to evaluate its effectiveness. We found cell-type-specific elements unique to each cell type investigated. These unique features show significant cell-type-specific biological relevance and tend to be located within functional regulatory elements. These results demonstrate the power of a differential comparative epigenomic strategy in deciphering the human genome and characterizing cell specificity.
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Registered trials
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