ArticleGenome biology2016
ChromNet: Learning the human chromatin network from all ENCODE ChIP-seq data.
Article in Genome biology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
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
18 citing papers in PubMed.
- BPGM as an intrinsic brake to constrain metastasis through phospho-epigenetic-mediated carnitine biosynthesis suppression.Neoplasia (New York, N.Y.) · 2026Article
- Unlocking hematopoietic stem cell potential: integrative computational approaches for genomic and transcriptomic analysis.Frontiers in cell and developmental biology · 2025Review
- Rescuing biologically relevant consensus regions across replicated samples.BMC bioinformatics · 2023Article
- Virtual ChIP-seq: predicting transcription factor binding by learning from the transcriptome.Genome biology · 2022Article
- Review
- A pathogenic DYT-THAP1 dystonia mutation causes hypomyelination and loss of YY1 binding.Human molecular genetics · 2022Article
- proChIPdb: a chromatin immunoprecipitation database for prokaryotic organisms.Nucleic acids research · 2022Article
- MYC protein interactors in gene transcription and cancer.Nature reviews. Cancer · 2021Review
- CpG content-dependent associations between transcription factors and histone modifications.PloS one · 2021Article
- Machine Learning for Integrating Data in Biology and Medicine: Principles, Practice, and Opportunities.An international journal on information fusion · 2019Article
- AIControl: replacing matched control experiments with machine learning improves ChIP-seq peak identification.Nucleic acids research · 2019Article
- Hierarchical cooperation of transcription factors from integration analysis of DNA sequences, ChIP-Seq and ChIA-PET data.BMC genomics · 2019Article
- Iterative random forests to discover predictive and stable high-order interactions.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- A graphical model approach visualizes regulatory relationships between genome-wide transcription factor binding profiles.Briefings in bioinformatics · 2018Article
- Probing instructions for expression regulation in gene nucleotide compositions.PLoS computational biology · 2018Article
- Chromosomal Conformations and Epigenomic Regulation in Schizophrenia.Progress in molecular biology and translational science · 2018Review
- The epigenomics of schizophrenia, in the mouse.American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics · 2017Review
- Boundaries of loop domains (insulators): Determinants of chromosome form and function in multicellular eukaryotes.BioEssays : news and reviews in molecular, cellular and developmental biology · 2017Review
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
A cell's epigenome arises from interactions among regulatory factors-transcription factors and histone modifications-co-localized at particular genomic regions. We developed a novel statistical method, ChromNet, to infer a network of these interactions, the chromatin network, by inferring conditional-dependence relationships among a large number of ChIP-seq data sets. We applied ChromNet to all available 1451 ChIP-seq data sets from the ENCODE Project, and showed that ChromNet revealed previously known physical interactions better than alternative approaches. We experimentally validated one of the previously unreported interactions, MYC-HCFC1. An interactive visualization tool is available at http://chromnet.cs.washington.edu.
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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.