ArticleNucleic acids research2011
Combinatorial chromatin modification patterns in the human genome revealed by subspace clustering.
Article in Nucleic acids research, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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25 citing papers in PubMed, 55 citations in OpenAlex.
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- Study on the spatial distribution patterns of histone modifications in Hippo pathway genes.Biophysics reports · 2021Article
- Self-organizing maps with variable neighborhoods facilitate learning of chromatin accessibility signal shapes associated with regulatory elements.BMC bioinformatics · 2021Article
- TriPCE: A Novel Tri-Clustering Algorithm for Identifying Pan-Cancer Epigenetic Patterns.Frontiers in genetics · 2019Article
- HebbPlot: an intelligent tool for learning and visualizing chromatin mark signatures.BMC bioinformatics · 2018Article
- Histone deacetylase inhibition modulates histone acetylation at gene promoter regions and affects genome-wide gene transcription in Schistosoma mansoni.PLoS neglected tropical diseases · 2017Article
- Dynamic epigenetic mode analysis using spatial temporal clustering.BMC bioinformatics · 2016Article
- Identification of recurrent combinatorial patterns of chromatin modifications at promoters across various tissue types.BMC bioinformatics · 2016Article
- ChARM: Discovery of combinatorial chromatin modification patterns in hepatitis B virus X-transformed mouse liver cancer using association rule mining.BMC bioinformatics · 2016Article
- Progress and challenges in bioinformatics approaches for enhancer identification.Briefings in bioinformatics · 2016Review
- Human endogenous retroviruses sustain complex and cooperative regulation of gene-containing loci and unannotated megabase-sized regions.Retrovirology · 2015Article
- A stationary wavelet entropy-based clustering approach accurately predicts gene expression.Journal of computational biology : a journal of computational molecular cell biology · 2015Article
- Spectacle: fast chromatin state annotation using spectral learning.Genome biology · 2015Article
- Modelling epigenetic regulation of gene expression in 12 human cell types reveals combinatorial patterns of cell-type-specific genes.IET systems biology · 2014Article
- The role of epigenetics in the biology of multiple myeloma.Blood cancer journal · 2014Review
- A wavelet-based method to exploit epigenomic language in the regulatory region.Bioinformatics (Oxford, England) · 2014Article
- Combinatorial epigenetic patterns as quantitative predictors of chromatin biology.BMC genomics · 2014Article
- A nucleosomal approach to inferring causal relationships of histone modifications.BMC genomics · 2014Article
- Discovery of cell-type specific regulatory elements in the human genome using differential chromatin modification analysis.Nucleic acids research · 2013Article
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3 authors at 1 institution in 1 country.
Funding
Abstract
Chromatin modifications, such as post-translational modification of histone proteins and incorporation of histone variants, play an important role in regulating gene expression. Joint analyses of multiple histone modification maps are starting to reveal combinatorial patterns of modifications that are associated with functional DNA elements, providing support to the 'histone code' hypothesis. However, due to the lack of analytical methods, only a small number of chromatin modification patterns have been discovered so far. Here, we introduce a scalable subspace clustering algorithm, coherent and shifted bicluster identification (CoSBI), to exhaustively identify the set of combinatorial modification patterns across a given epigenome. Performance comparisons demonstrate that CoSBI can generate biclusters with higher intra-cluster coherency and biological relevance. We apply our algorithm to a compendium of 39 genome-wide chromatin modification maps in human CD4(+) T cells. We identify 843 combinatorial patterns that recur at >0.1% of the genome. A total of 19 chromatin modifications are observed in the combinatorial patterns, 10 of which occur in more than half of the patterns. We also identify combinatorial modification signatures for eight classes of functional DNA elements. Application of CoSBI to epigenome maps of different cells and developmental stages will aid in understanding how chromatin structure helps regulate gene expression.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.