ArticleNucleic acids research2013
Integrative annotation of chromatin elements from ENCODE data.
Article in Nucleic acids research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 336 papers, 5 of them syntheses that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
336 citing papers in PubMed, 5 syntheses or guidelines pooled it, 619 citations in OpenAlex.
- Trans-Ancestral Fine-Mapping and Epigenetic Annotation as Tools to Delineate Functionally Relevant Risk Alleles atInternational journal of molecular sciences · 2020Pooled it
- Meta-analysis of massively parallel reporter assays enables prediction of regulatory function across cell types.Human mutation · 2019Pooled it
- Integrative genomic analysis predicts novel functional enhancer-SNPs for bone mineral density.Human genetics · 2019Pooled it
- Fine-mapping of prostate cancer susceptibility loci in a large meta-analysis identifies candidate causal variants.Nature communications · 2018Pooled it
- Germline variation in ADAMTSL1 is associated with prognosis following breast cancer treatment in young women.Nature communications · 2017Pooled it
- Pan-cancer multi-omics analysis reveals upregulation of the POLE2 subunit of DNA polymerase epsilon and its associations with patient survival and cellular pathways beyond DNA replication.NAR genomics and bioinformatics · 2026Article
- Functional Annotation of GWAS Loci Using Public Transcriptome and Epigenome Datasets Reveals Non-Coding Genes and Regulatory Elements Which May Contribute to BMI.International journal of molecular sciences · 2026Article
- Pan-cell type continuous chromatin state annotation of 1,698 epigenomes from the International Human Epigenome Consortium.Genome biology · 2026Article
- Pervasive cryptic selection in the human noncoding genome.bioRxiv : the preprint server for biology · 2026Article
- Predictive modeling of signal-responsive cis-elements in human red blood cell precursors.Nucleic acids research · 2026Article
- Genetic Signal Augmentation of Childhood-Onset and Treatment-Resistant Major Depression Reveals Distinct Biological Disorders.medRxiv : the preprint server for health sciences · 2026Article
- Beyond blacklists: a critical assessment of exclusion set generation strategies and alternative approaches.Bioinformatics (Oxford, England) · 2026Article
- MiniPromoters Ple384 (TH) and Ple388 (PITX3) for targeting midbrain dopaminergic neurons in mice and monkeys.Scientific reports · 2026Article
- Epigenetic and Transcriptional Programs Define Osteosarcoma Subtypes and Establish Targetable Vulnerabilities.Cancer discovery · 2026Article
- Chromatin state dynamics during the Plasmodium falciparum intraerythrocytic development cycle.BMC genomics · 2026Article
- 3D genome folding in epigenetic regulation and cellular memory.Trends in cell biology · 2026Review
- Targeting the 3D genome by anthracyclines for chemotherapeutic effects.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Beyond Blacklists: A Critical Assessment of Exclusion Set Generation Strategies and Alternative Approaches.bioRxiv : the preprint server for biology · 2025Article
- Article
- Uncovering methylation-dependent genetic effects on regulatory element function in diverse genomes.Genome research · 2025Article
276 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
14 authors at 6 institutions in 2 countries.
Funding
Abstract
The ENCODE Project has generated a wealth of experimental information mapping diverse chromatin properties in several human cell lines. Although each such data track is independently informative toward the annotation of regulatory elements, their interrelations contain much richer information for the systematic annotation of regulatory elements. To uncover these interrelations and to generate an interpretable summary of the massive datasets of the ENCODE Project, we apply unsupervised learning methodologies, converting dozens of chromatin datasets into discrete annotation maps of regulatory regions and other chromatin elements across the human genome. These methods rediscover and summarize diverse aspects of chromatin architecture, elucidate the interplay between chromatin activity and RNA transcription, and reveal that a large proportion of the genome lies in a quiescent state, even across multiple cell types. The resulting annotation of non-coding regulatory elements correlate strongly with mammalian evolutionary constraint, and provide an unbiased approach for evaluating metrics of evolutionary constraint in human. Lastly, we use the regulatory annotations to revisit previously uncharacterized disease-associated loci, resulting in focused, testable hypotheses through the lens of the chromatin landscape.
Indexed as
Identifiers
What OpenQuestion holds
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.