ArticleGenome research2007
Identification of higher-order functional domains in the human ENCODE regions.
Article in Genome research, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 83 papers.
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
83 citing papers in PubMed.
- Landscape of the Epstein-Barr virus-host chromatin interactome and gene regulation.The EMBO journal · 2025Article
- Evaluating topography of mutational signatures with SigProfilerTopography.Genome biology · 2025Article
- DNA replication timing reveals genome-wide features of transcription and fragility.Nature communications · 2025Article
- Precision and efficacy of RNA-guided DNA integration in high-expressing muscle loci.Molecular therapy. Nucleic acids · 2024Article
- Inferring replication timing and proliferation dynamics from single-cell DNA sequencing data.Nature communications · 2024Article
- scAbsolute: measuring single-cell ploidy and replication status.Genome biology · 2024Article
- Logical design of synthetic cis-regulatory DNA for genetic tracing of cell identities and state changes.Nature communications · 2024Article
- Single-molecule genome-wide mutation profiles of cell-free DNA for non-invasive detection of cancer.Nature genetics · 2023Article
- Article
- Neural network and kinetic modelling of human genome replication reveal replication origin locations and strengths.PLoS computational biology · 2023Article
- Integrative chromatin domain annotation through graph embedding of Hi-C data.Bioinformatics (Oxford, England) · 2023Article
- New Approaches to Assess Mechanisms of Action of Selective Vitamin D Analogues.International journal of molecular sciences · 2021Review
- Asymmetrical deposition and modification of histone H3 variants are essential for zygote development.Life science alliance · 2021Article
- Learning mutational signatures and their multidimensional genomic properties with TensorSignatures.Nature communications · 2021Article
- Genetic-variant hotspots and hotspot clusters in the human genome facilitating adaptation while increasing instability.Human genomics · 2021Article
- Common Threads: Aphidicolin-Inducible and Folate-Sensitive Fragile Sites in the Human Genome.Frontiers in genetics · 2021Review
- Multiomics Analysis of Neuroblastoma Cells Reveals a Diversity of Malignant Transformations.Frontiers in cell and developmental biology · 2021Article
- XPC deficiency increases risk of hematologic malignancies through mutator phenotype and characteristic mutational signature.Nature communications · 2020Article
- Synchronized replication of genes encoding the same protein complex in fast-proliferating cells.Genome research · 2019Article
- A unified encyclopedia of human functional DNA elements through fully automated annotation of 164 human cell types.Genome biology · 2019Article
23 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
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
It has long been posited that human and other large genomes are organized into higher-order (i.e., greater than gene-sized) functional domains. We hypothesized that diverse experimental data types generated by The ENCODE Project Consortium could be combined to delineate active and quiescent or repressed functional domains and thereby illuminate the higher-order functional architecture of the genome. To address this, we coupled wavelet analysis with hidden Markov models for unbiased discovery of "domain-level" behavior in high-resolution functional genomic data, including activating and repressive histone modifications, RNA output, and DNA replication timing. We find that higher-order patterns in these data types are largely concordant and may be analyzed collectively in the context of HeLa cells to delineate 53 active and 62 repressed functional domains within the ENCODE regions. Active domains comprise approximately 44% of the ENCODE regions but contain approximately 75%-80% of annotated genes, transcripts, and CpG islands. Repressed domains are enriched in certain classes of repetitive elements and, surprisingly, in evolutionarily conserved nonexonic sequences. The functional domain structure of the ENCODE regions appears to be largely stable across different cell types. Taken together, our results suggest that higher-order functional domains represent a fundamental organizing principle of human genome architecture.
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.