ArticleNature communications2015
Systematic chromatin state comparison of epigenomes associated with diverse properties including sex and tissue type.
Article in Nature communications, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers, 2 of them syntheses that pooled it.
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Who cites it
40 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Sex-specific DNA methylation differences in Alzheimer's disease pathology.Acta neuropathologica communications · 2021Pooled it
- Epigenome-wide meta-analysis of DNA methylation differences in prefrontal cortex implicates the immune processes in Alzheimer's disease.Nature communications · 2020Pooled it
- From aging to Alzheimer's disease: concordant brain DNA methylation changes in late life.Genome medicine · 2026Article
- chromIDEAS reveals epigenetic dynamics via multi-dimensional clustering of chromatin states.Nucleic acids research · 2026Article
- Dynamic allele usage of X-linked genes ameliorates neurodevelopmental disease phenotypes in brain organoids.Nature communications · 2026Article
- The Rayleigh Quotient and Contrastive Principal Component Analysis I.bioRxiv : the preprint server for biology · 2025Article
- Epilogos: information-theoretic navigation of multi-tissue functional genomic annotations.bioRxiv : the preprint server for biology · 2025Article
- Article
- Robust chromatin state annotation.Genome research · 2024Article
- Integrative mapping of the dog epigenome: Reference annotation for comparative intertissue and cross-species studies.Science advances · 2023Article
- Universal chromatin state annotation of the mouse genome.Genome biology · 2023Article
- Histone Maps inInternational journal of molecular sciences · 2023Article
- A framework for group-wise summarization and comparison of chromatin state annotations.Bioinformatics (Oxford, England) · 2023Article
- Computational methods to explore chromatin state dynamics.Briefings in bioinformatics · 2022Review
- Article
- Chromatin landscape associated with sexual differentiation in a UV sex determination system.Nucleic acids research · 2022Article
- PlantGSAD: a comprehensive gene set annotation database for plant species.Nucleic acids research · 2022Article
- Reprogramming of H3K9bhb at regulatory elements is a key feature of fasting in the small intestine.Cell reports · 2021Article
- Skeletal muscle methylome and transcriptome integration reveals profound sex differences related to muscle function and substrate metabolism.Clinical epigenetics · 2021Article
- Predict long-range enhancer regulation based on protein-protein interactions between transcription factors.Nucleic acids research · 2021Article
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2 authors.
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Abstract
Epigenomic data sets provide critical information about the dynamic role of chromatin states in gene regulation, but a key question of how chromatin state segmentations vary under different conditions across the genome has remained unaddressed. Here we present ChromDiff, a group-wise chromatin state comparison method that generates an information-theoretic representation of epigenomes and corrects for external covariate factors to better isolate relevant chromatin state changes. By applying ChromDiff to the 127 epigenomes from the Roadmap Epigenomics and ENCODE projects, we provide novel group-wise comparative analyses across sex, tissue type, state and developmental age. Remarkably, we find that distinct sets of epigenomic features are maximally discriminative for different group-wise comparisons, in each case revealing distinct enriched pathways, many of which do not show gene expression differences. Our methodology should be broadly applicable for epigenomic comparisons and provides a powerful new tool for studying chromatin state differences at the genome scale.
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