ReviewAnnual review of genetics2014
pENCODE: a plant encyclopedia of DNA elements.
Review in Annual review of genetics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 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
24 citing papers in PubMed.
- Epigenetic crop improvement: Integrating ENCODE strategies into horticultural breeding.Horticulture research · 2025Article
- DeepWheat: predicting the effects of genomic variants on gene expression and regulatory activities across tissues and varieties in wheat using deep learning.Genome biology · 2025Article
- Genetic variation at transcription factor binding sites largely explains phenotypic heritability in maize.Nature genetics · 2025Article
- Epigenomic and 3D genomic mapping reveals developmental dynamics and subgenomic asymmetry of transcriptional regulatory architecture in allotetraploid cotton.Nature communications · 2024Article
- Phenotype prediction in plants is improved by integrating large-scale transcriptomic datasets.NAR genomics and bioinformatics · 2024Article
- Review
- aChIP is an efficient and sensitive ChIP-seq technique for economically important plant organs.Nature plants · 2024Article
- aChIP for comprehensive chromatin profiling in economically important plant organs.Nature plants · 2024Article
- Application of Single-Cell Assay for Transposase-Accessible Chromatin with High Throughput Sequencing in Plant Science: Advances, Technical Challenges, and Prospects.International journal of molecular sciences · 2024Review
- Integrating omics databases for enhanced crop breeding.Journal of integrative bioinformatics · 2023Review
- Epigenomics in stress tolerance of plants under the climate change.Molecular biology reports · 2023Review
- The ChIP-Hub Resource: Toward plantEncode.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Inferring regulatory element landscapes and gene regulatory networks from integrated analysis in eight hulless barley varieties under abiotic stress.BMC genomics · 2022Article
- Deciphering the Epigenetic Alphabet Involved in Transgenerational Stress Memory in Crops.International journal of molecular sciences · 2021Review
- Stable unmethylated DNA demarcates expressed genes and their cis-regulatory space in plant genomes.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Epigenetics: possible applications in climate-smart crop breeding.Journal of experimental botany · 2020Review
- Plant science decadal vision 2020-2030: Reimagining the potential of plants for a healthy and sustainable future.Plant direct · 2020Article
- The regulatory landscape of early maize inflorescence development.Genome biology · 2020Article
- Integrative analysis of reference epigenomes in 20 rice varieties.Nature communications · 2020Article
- DNA methylation footprints during soybean domestication and improvement.Genome biology · 2018Article
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
Abstract
ENCODE projects exist for many eukaryotes, including humans, but as of yet no defined project exists for plants. A plant ENCODE would be invaluable to the research community and could be more readily produced than its metazoan equivalents by capitalizing on the preexisting infrastructure provided from similar projects. Collecting and normalizing plant epigenomic data for a range of species will facilitate hypothesis generation, cross-species comparisons, annotation of genomes, and an understanding of epigenomic functions throughout plant evolution. Here, we discuss the need for such a project, outline the challenges it faces, and suggest ways forward to build a plant ENCODE.
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.