ArticleNucleic acids research2014
Inference of interactions between chromatin modifiers and histone modifications: from ChIP-Seq data to chromatin-signaling.
Article in Nucleic acids research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- Foundation model reveals the shared organization of transcription and topologically associating domains.Cell systems · 2026Article
- The reprogramming and function of H4K20me1 during early embryo development.EMBO reports · 2026Article
- An Introduction to Network Analysis in Plant Biology.Plant direct · 2025Article
- Modelling transcription with explainable AI uncovers context-specific epigenetic gene regulation at promoters and gene bodies.PLoS genetics · 2025Article
- Mutant EZH2 alters the epigenetic network and increases epigenetic heterogeneity in B cell lymphoma.PLoS biology · 2025Article
- asteRIa enables robust interaction modeling between chromatin modifications and epigenetic readers.Nucleic acids research · 2024Article
- CpG content-dependent associations between transcription factors and histone modifications.PloS one · 2021Article
- AIControl: replacing matched control experiments with machine learning improves ChIP-seq peak identification.Nucleic acids research · 2019Article
- The Distance Precision Matrix: computing networks from non-linear relationships.Bioinformatics (Oxford, England) · 2019Article
- Relationship between epigenetic changes in Wnt antagonists and acute leukemia.Oncology reports · 2017Article
- Role of the chromatin landscape and sequence in determining cell type-specific genomic glucocorticoid receptor binding and gene regulation.Nucleic acids research · 2017Article
- Transcription factors, coregulators, and epigenetic marks are linearly correlated and highly redundant.PloS one · 2017Article
- ChromNet: Learning the human chromatin network from all ENCODE ChIP-seq data.Genome biology · 2016Article
- Chromas from chromatin: sonification of the epigenome.F1000Research · 2016Article
- eRFSVM: a hybrid classifier to predict enhancers-integrating random forests with support vector machines.Hereditas · 2016Article
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Authors and funding
5 authors.
Funding
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Abstract
Chromatin modifiers and histone modifications are components of a chromatin-signaling network involved in transcription and its regulation. The interactions between chromatin modifiers and histone modifications are often unknown, are based on the analysis of few genes or are studied in vitro. Here, we apply computational methods to recover interactions between chromatin modifiers and histone modifications from genome-wide ChIP-Seq data. These interactions provide a high-confidence backbone of the chromatin-signaling network. Many recovered interactions have literature support; others provide hypotheses about yet unknown interactions. We experimentally verified two of these predicted interactions, leading to a link between H4K20me1 and members of the Polycomb Repressive Complexes 1 and 2. Our results suggest that our computationally derived interactions are likely to lead to novel biological insights required to establish the connectivity of the chromatin-signaling network involved in transcription and its regulation.
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