ArticleGenome research2008
Inferring causal relationships among different histone modifications and gene expression.
Article in Genome research, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 59 papers.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
59 citing papers in PubMed.
- Article
- Bayesian networks for network inference in biology.Journal of the Royal Society, Interface · 2025Review
- Coregulatory effects of multiple histone modifications in key ferroptosis-related genes for lung adenocarcinoma.Epigenomics · 2024Article
- MAT2A inhibition suppresses inflammation inJournal of oral microbiology · 2024Article
- Human PBMC scRNA-seq-based aging clocks reveal ribosome to inflammation balance as a single-cell aging hallmark and super longevity.Science advances · 2023Article
- KCNQ1OT1 promotes genome-wide transposon repression by guiding RNA-DNA triplexes and HP1 binding.Nature cell biology · 2022Article
- Dissecting cell fate dynamics in pediatric glioblastoma through the lens of complex systems and cellular cybernetics.Biological cybernetics · 2022Review
- Specific histone modifications associate with alternative exon selection during mammalian development.Nucleic acids research · 2020Article
- A comprehensive review of computational prediction of genome-wide features.Briefings in bioinformatics · 2020Article
- Histone Methylation Mechanisms Modulate the Inflammatory Response of Periodontal Ligament Progenitors.Stem cells and development · 2019Article
- Combinatorial Pattern of Histone Modifications in Exon Skipping Event.Frontiers in genetics · 2019Article
- Revealing transcription factor and histone modification co-localization and dynamics across cell lines by integrating ChIP-seq and RNA-seq data.BMC genomics · 2018Article
- Sequence-based 5-mers highly correlated to epigenetic modifications in genes interactions.Genes & genomics · 2018Article
- Inter-nucleosomal communication between histone modifications for nucleosome phasing.PLoS computational biology · 2018Article
- Single-cell, single-mRNA analysis of Ccnb1 promoter regulation.Scientific reports · 2017Article
- Transcription factors, coregulators, and epigenetic marks are linearly correlated and highly redundant.PloS one · 2017Article
- ChARM: Discovery of combinatorial chromatin modification patterns in hepatitis B virus X-transformed mouse liver cancer using association rule mining.BMC bioinformatics · 2016Article
- Integrating Epigenomics into the Understanding of Biomedical Insight.Bioinformatics and biology insights · 2016Review
- Endotoxin tolerance in monocytes can be mitigated by α2-interferon.Journal of leukocyte biology · 2015Article
- Large-scale imputation of epigenomic datasets for systematic annotation of diverse human tissues.Nature biotechnology · 2015Article
Corrections and comments
- Erratum issued
Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Histone modifications are major epigenetic factors regulating gene expression. They play important roles in maintaining stem cell pluripotency and in cancer pathogenesis. Different modifications may combine to form complex "histone codes." Recent high-throughput technologies, such as "ChIP-chip" and "ChIP-seq," have generated high-resolution maps for many histone modifications on the human genome. Here we use these maps to build a Bayesian network to infer causal and combinatorial relationships among histone modifications and gene expression. A pilot network derived by the same method among polycomb group (PcG) genes and H3K27 trimethylation is accurately supported by current literature. Our unbiased network model among histone modifications is also well supported by cross-validation results. It not only confirmed already known relationships, such as those of H3K27me3 to gene silencing, H3K4me3 to gene activation and the effect of bivalent modification of both H3K4me3 and H3K27me3, but also identified many other relationships that may predict new epigenetic interactions important in epigenetic gene regulation. Our automated inference method, which is potentially applicable to other ChIP-chip or ChIP-seq data analyses, provides a much-needed guide to deciphering the complex histone codes.
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Registered trials
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.