ArticleJournal of bacteriology2011
Inference of the transcriptional regulatory network in Staphylococcus aureus by integration of experimental and genomics-based evidence.
Article in Journal of bacteriology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers, 1 of them a synthesis that pooled it.
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
32 citing papers in PubMed, 1 synthesis or guideline pooled it, 49 citations in OpenAlex.
- Evolution of transcriptional regulation of histidine metabolism in Gram-positive bacteria.BMC genomics · 2022Pooled it
- Bioinformatics in Russia: history and present-day landscape.Briefings in bioinformatics · 2024Review
- Histidine transport is essential for the growth of Staphylococcus aureus at low pH.PLoS pathogens · 2024Article
- A genetic regulatory see-saw of biofilm and virulence in MRSA pathogenesis.Frontiers in microbiology · 2023Review
- From a large-scale genomic analysis of insertion sequences to insights into their regulatory roles in prokaryotes.BMC genomics · 2022Article
- Homology-based reconstruction of regulatory networks for bacterial and archaeal genomes.Frontiers in microbiology · 2022Article
- The gene regulatory network ofFrontiers in microbiology · 2022Article
- Limiting protease production plays a key role in the pathogenesis of the divergent clinical isolates ofVirulence · 2021Article
- Revealing 29 sets of independently modulated genes inProceedings of the National Academy of Sciences of the United States of America · 2020Article
- Article
- Comparative Genomics Reveals the Regulatory Complexity of Bifidobacterial Arabinose and Arabino-Oligosaccharide Utilization.Frontiers in microbiology · 2018Article
- Review
- Heme Synthesis and Acquisition in Bacterial Pathogens.Journal of molecular biology · 2016Review
- Regulatory Requirements for Staphylococcus aureus Nitric Oxide Resistance.Journal of bacteriology · 2016Article
- Comparative genomics and evolution of transcriptional regulons inMicrobial genomics · 2016Article
- Staphylococcus aureus Transcriptome Architecture: From Laboratory to Infection-Mimicking Conditions.PLoS genetics · 2016Article
- Comparative genomics of pyridoxal 5'-phosphate-dependent transcription factor regulons inMicrobial genomics · 2016Article
- Transcriptional Regulation of Carbohydrate Utilization Pathways in the Bifidobacterium Genus.Frontiers in microbiology · 2016Article
- Cautions about the reliability of pairwise gene correlations based on expression data.Frontiers in microbiology · 2015Article
- Comparative genomics and evolution of regulons of the LacI-family transcription factors.Frontiers in microbiology · 2014Article
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 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Transcriptional regulatory networks are fine-tuned systems that help microorganisms respond to changes in the environment and cell physiological state. We applied the comparative genomics approach implemented in the RegPredict Web server combined with SEED subsystem analysis and available information on known regulatory interactions for regulatory network reconstruction for the human pathogen Staphylococcus aureus and six related species from the family Staphylococcaceae. The resulting reference set of 46 transcription factor regulons contains more than 1,900 binding sites and 2,800 target genes involved in the central metabolism of carbohydrates, amino acids, and fatty acids; respiration; the stress response; metal homeostasis; drug and metal resistance; and virulence. The inferred regulatory network in S. aureus includes ∼320 regulatory interactions between 46 transcription factors and ∼550 candidate target genes comprising 20% of its genome. We predicted ∼170 novel interactions and 24 novel regulons for the control of the central metabolic pathways in S. aureus. The reconstructed regulons are largely variable in the Staphylococcaceae: only 20% of S. aureus regulatory interactions are conserved across all studied genomes. We used a large-scale gene expression data set for S. aureus to assess relationships between the inferred regulons and gene expression patterns. The predicted reference set of regulons is captured within the Staphylococcus collection in the RegPrecise database (http://regprecise.lbl.gov).
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.