ArticleNucleic acids research2014
DOOR 2.0: presenting operons and their functions through dynamic and integrated views.
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 110 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
110 citing papers in PubMed.
- Functions of the prp operon in carbon source metabolism and acetic acid resistance in acetic acid bacteria: a case study in Acetobacter pasteurianus CGMCC 1.41.BMC microbiology · 2026Article
- Transformer-based operon prediction using textual representations of gene pairs.Bioinformatics advances · 2026Article
- CRISPRi screening revealsmSystems · 2025Article
- Rationally designed pooled CRISPRi-seq uncovers an inhibitor of bacterial peptidyl-tRNA hydrolase.Cell reports · 2024Article
- The Transcriptomic Response of Cells of the Thermophilic BacteriumInternational journal of molecular sciences · 2024Article
- Function of Burkholderia pseudomallei RpoS and RpoN2 in bacterial invasion, intracellular survival, and multinucleated giant cell formation in mouse macrophage cell line.Antonie van Leeuwenhoek · 2024Article
- Noncontiguous operon atlas for themicroLife · 2024Article
- Microbial Cell Factories in the Bioeconomy Era: From Discovery to Creation.Biodesign research · 2024Review
- The Escherichia coli Fur pan-regulon has few conserved but many unique regulatory targets.Nucleic acids research · 2023Article
- The transcriptional regulator EarA and intergenic terminator sequences modulate archaellation inFrontiers in microbiology · 2023Article
- Article
- The endogenous Coxiella burnetii plasmid encodes a functional toxin-antitoxin system.Molecular microbiology · 2022Article
- Article
- Systematic analysis of the underlying genomic architecture for transcriptional-translational coupling in prokaryotes.NAR genomics and bioinformatics · 2022Article
- OperonSEQer: A set of machine-learning algorithms with threshold voting for detection of operon pairs using short-read RNA-sequencing data.PLoS computational biology · 2022Article
- Article
- Cappable-Seq Reveals Specific Patterns of Metabolism and Virulence forInternational journal of molecular sciences · 2021Article
- Identification and characterization of proteins of unknown function (PUFs) in Clostridium thermocellum DSM 1313 strains as potential genetic engineering targets.Biotechnology for biofuels · 2021Article
- Pathogenic Determinants of theMicroorganisms · 2021Article
- Detecting operons in bacterial genomes via visual representation learning.Scientific reports · 2021Article
50 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
9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We have recently developed a new version of the DOOR operon database, DOOR 2.0, which is available online at http://csbl.bmb.uga.edu/DOOR/ and will be updated on a regular basis. DOOR 2.0 contains genome-scale operons for 2072 prokaryotes with complete genomes, three times the number of genomes covered in the previous version published in 2009. DOOR 2.0 has a number of new features, compared with its previous version, including (i) more than 250,000 transcription units, experimentally validated or computationally predicted based on RNA-seq data, providing a dynamic functional view of the underlying operons; (ii) an integrated operon-centric data resource that provides not only operons for each covered genome but also their functional and regulatory information such as their cis-regulatory binding sites for transcription initiation and termination, gene expression levels estimated based on RNA-seq data and conservation information across multiple genomes; (iii) a high-performance web service for online operon prediction on user-provided genomic sequences; (iv) an intuitive genome browser to support visualization of user-selected data; and (v) a keyword-based Google-like search engine for finding the needed information intuitively and rapidly in this database.
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.