ArticleBMC genomics2013
RegTransBase--a database of regulatory sequences and interactions based on literature: a resource for investigating transcriptional regulation in prokaryotes.
Article in BMC genomics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 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
41 citing papers in PubMed, 92 citations in OpenAlex.
- Unveiling the landscape of prokaryotic global regulators through deep protein language models.mSystems · 2025Article
- Biological Switches: Past and Future Milestones of Transcription Factor-Based Biosensors.ACS synthetic biology · 2025Review
- Bioinformatics in Russia: history and present-day landscape.Briefings in bioinformatics · 2024Review
- Systematic elucidation of independently modulated genes in Lactiplantibacillus plantarum reveals a trade-off between secondary and primary metabolism.Microbial biotechnology · 2024Article
- Comparative Genomics ofPHAGE (New Rochelle, N.Y.) · 2023Article
- Mutation Analysis in Regulator DNA-Binding Regions for Antimicrobial Efflux Pumps in 17,000Microorganisms · 2023Article
- Independent Component Analysis Reveals the Transcriptional Regulatory Modules inInternational journal of molecular sciences · 2023Article
- Sensbio: an online server for biosensor design.BMC bioinformatics · 2023Article
- From a large-scale genomic analysis of insertion sequences to insights into their regulatory roles in prokaryotes.BMC genomics · 2022Article
- Curation, inference, and assessment of a globally reconstructed gene regulatory network for Streptomyces coelicolor.Scientific reports · 2022Article
- Cell-Free Biosensors and AI Integration.Methods in molecular biology (Clifton, N.J.) · 2022Article
- High-pressure processing-induced transcriptome response during recovery of Listeria monocytogenes.BMC genomics · 2021Article
- Transcriptomic time-series analysis of cold- and heat-shock response in psychrotrophic lactic acid bacteria.BMC genomics · 2021Article
- A Förster Resonance Energy Transfer-Based Ratiometric Sensor with the Allosteric Transcription Factor TetR.Small (Weinheim an der Bergstrasse, Germany) · 2020Article
- RhizoBindingSites, a Database of DNA-Binding Motifs in Nitrogen-Fixing Bacteria Inferred Using a Footprint Discovery Approach.Frontiers in microbiology · 2020Article
- The BioCyc collection of microbial genomes and metabolic pathways.Briefings in bioinformatics · 2019Article
- Systematic approach for dissecting the molecular mechanisms of transcriptional regulation in bacteria.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- A dataset of small molecules triggering transcriptional and translational cellular responses.Data in brief · 2018Article
- Differential RNA Sequencing Implicates Sulfide as the Master Regulator of SApplied and environmental microbiology · 2018Article
- Tailor-made transcriptional biosensors for optimizing microbial cell factories.Journal of industrial microbiology & biotechnology · 2017Review
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 5 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundDue to the constantly growing number of sequenced microbial genomes, comparative genomics has been playing a major role in the investigation of regulatory interactions in bacteria. Regulon inference mostly remains a field of semi-manual examination since absence of a knowledgebase and informatics platform for automated and systematic investigation restricts opportunities for computational prediction. Additionally, confirming computationally inferred regulons by experimental data is critically important. DESCRIPTION: RegTransBase is an open-access platform with a user-friendly web interface publicly available at http://regtransbase.lbl.gov. It consists of two databases - a manually collected hierarchical regulatory interactions database based on more than 7000 scientific papers which can serve as a knowledgebase for verification of predictions, and a large set of curated by experts transcription factor binding sites used in regulon inference by a variety of tools. RegTransBase captures the knowledge from published scientific literature using controlled vocabularies and contains various types of experimental data, such as: the activation or repression of transcription by an identified direct regulator; determination of the transcriptional regulatory function of a protein (or RNA) directly binding to DNA or RNA; mapping of binding sites for a regulatory protein; characterization of regulatory mutations. Analysis of the data collected from literature resulted in the creation of Putative Regulons from Experimental Data that are also available in RegTransBase.
conclusionsRegTransBase is a powerful user-friendly platform for the investigation of regulation in prokaryotes. It uses a collection of validated regulatory sequences that can be easily extracted and used to infer regulatory interactions by comparative genomics techniques thus assisting researchers in the interpretation of transcriptional regulation data.
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.