ArticleCurrent protocols in bioinformatics2018
Using RegulonDB, the Escherichia coli K-12 Gene Regulatory Transcriptional Network Database.
Article in Current protocols in bioinformatics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 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
10 citing papers in PubMed, 12 citations in OpenAlex.
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- FGeneBERT: function-driven pre-trained gene language model for metagenomics.Briefings in bioinformatics · 2025Article
- A Causal Regulation Modeling Algorithm for Temporal Events with Application toInternational journal of molecular sciences · 2024Article
- Genomic language model predicts protein co-regulation and function.Nature communications · 2024Article
- Article
- Distinct heterochromatin-like domains promote transcriptional memory and silence parasitic genetic elements in bacteria.The EMBO journal · 2022Article
- PRODORIC: state-of-the-art database of prokaryotic gene regulation.Nucleic acids research · 2022Article
- The bacterial promoter spacer modulates promoter strength and timing by length, TG-motifs and DNA supercoiling sensitivity.Scientific reports · 2021Article
- Genomewide Stabilization of mRNA during a "Feast-to-Famine" Growth Transition in Escherichia coli.mSphere · 2020Article
- RegulonDB v 10.5: tackling challenges to unify classic and high throughput knowledge of gene regulation in E. coli K-12.Nucleic acids research · 2019Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors at 2 institutions in 1 country.
Funding
Abstract
In RegulonDB, for over 25 years, we have been gathering knowledge by manual curation from original scientific literature on the regulation of transcription initiation and genome organization in transcription units of the Escherichia coli K-12 genome. This unit describes six basic protocols that can serve as a guiding introduction to the main content of the current version (v9.4) of this electronic resource. These protocols include general navigation as well as searching for specific objects such as genes, gene products, transcription units, promoters, transcription factors, coexpression, and genetic sensory response units or GENSOR Units. In these protocols, the user will find an initial introduction to the concepts pertinent to the protocol, the content obtained when performing the given navigation, and the necessary resources for carrying out the protocol. This easy-to-follow presentation should help anyone interested in quickly seeing all that is currently offered in RegulonDB, including position weight matrices of transcription factors, coexpression values based on published microarrays, and the GENSOR Units unique to RegulonDB that offer regulatory mechanisms in the context of their signals and metabolic consequences. © 2018 by John Wiley & Sons, Inc.
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.