ArticleNucleic acids research2014
ppdb: plant promoter database version 3.0.
Article in Nucleic acids research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 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
34 citing papers in PubMed.
- Synthetic Biology of Plants and Microbes for Agriculture, Environment, and Future Applications.Chemical reviews · 2026Review
- Identification and application of bioparts for plant synthetic biology.Molecules and cells · 2025Review
- Advancing ornamental plant breeding through genomic technologies: opportunities, challenges, and future directions.Functional & integrative genomics · 2025Review
- Structural insights into CDF1 accumulation on the CONSTANS promoter via a plant-specific DNA-binding domain.Nature plants · 2025Article
- The ChIP-Hub Resource: Toward plantEncode.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Plant Promoters and Terminators for High-Precision Bioengineering.Biodesign research · 2023Review
- Article
- Deciphering the molecular basis of tissue-specific gene expression in plants: Can synthetic biology help?Current opinion in plant biology · 2022Review
- Sequence-based evaluation of promoter context for prediction of transcription start sites in Arabidopsis and rice.Scientific reports · 2022Article
- Optogenetic and Chemical Induction Systems for Regulation of Transgene Expression in Plants: Use in Basic and Applied Research.International journal of molecular sciences · 2022Review
- Three regions of thePlant signaling & behavior · 2021Article
- Isolation of novel citrus and plum fruit promoters and their functional characterization for fruit biotechnology.BMC biotechnology · 2020Article
- Cytosolic GLUTAMINE SYNTHETASE1;1 Modulates Metabolism and Chloroplast Development in Roots.Plant physiology · 2020Article
- Article
- ThePlants (Basel, Switzerland) · 2019Article
- Completion of the cytosolic post-chorismate phenylalanine biosynthetic pathway in plants.Nature communications · 2019Article
- Prediction of auxin response elements based on data fusion in Arabidopsis thaliana.Molecular biology reports · 2018Article
- Identification of Two Auxin-Regulated Potassium Transporters Involved in Seed Maturation.International journal of molecular sciences · 2018Article
- Delineation of condition specific Cis- and Trans-acting elements in plant promoters under various Endo- and exogenous stimuli.BMC genomics · 2018Article
- Dempster-Shafer Theory for the Prediction of Auxin-Response Elements (AuxREs) in Plant Genomes.BioMed research international · 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
15 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
ppdb (http://ppdb.agr.gifu-u.ac.jp) is a plant promoter database that provides information on transcription start sites (TSSs), core promoter structure (TATA boxes, Initiators, Y Patches, GA and CA elements) and regulatory element groups (REGs) as putative and comprehensive transcriptional regulatory elements. Since the last report in this journal, the database has been updated in three areas to version 3.0. First, new genomes have been included in the database, and now ppdb provides information on Arabidopsis thaliana, rice, Physcomitrella patens and poplar. Second, new TSS tag data (34 million) from A. thaliana, determined by a high throughput sequencer, has been added to give a ∼200-fold increase in TSS data compared with version 1.0. This results in a much higher coverage of ∼27,000 A. thaliana genes and finer positioning of promoters even for genes with low expression levels. Third, microarray data-based predictions have been appended as REG annotations which inform their putative physiological roles.
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.