ArticleScientific reports2022
Transcriptomic profiling of Escherichia coli K-12 in response to a compendium of stressors.
Article in Scientific reports, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 19 papers, 1 of them a synthesis that pooled it.
What it found
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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
19 citing papers in PubMed, 1 synthesis or guideline pooled it, 27 citations in OpenAlex.
- Fitness costs of mobilised colistin resistance gene 3 (mcr-3): systematic review, epidemiological study, and functional analysis.EBioMedicine · 2025Pooled it
- Retention and biosynthesis of diverse nitroarenes in Escherichia coli after combinatorial nitroreductase gene deletions.Nature chemistry · 2026Article
- Stress-induced remodeling of yeast amino acid pools occurs within conserved physicochemical constraints.Folia microbiologica · 2026Article
- Oxalate-mediated detoxification and bioaccumulation of lead and cadmium inMicrobiology (Reading, England) · 2026Article
- Gene expression plasticity under multiple stresses drives higher tolerance to a macrolide in saline and warmer environments.npj antimicrobials and resistance · 2026Article
- Comparative transcriptomic analysis of perfluoroalkyl substances-induced responses of exponential and stationary phase Escherichia coli.BMC genomics · 2025Article
- Antibiotic-induced stress responses in Gram-negative bacteria and their role in antibiotic resistance.The Journal of antimicrobial chemotherapy · 2025Review
- A globular protein exhibits rare phase behavior and forms chemically regulated orthogonal condensates in cells.Nature communications · 2025Article
- Laboratory evolution ofJournal of bacteriology · 2025Article
- Adaptations ofACS omega · 2024Article
- The master regulator OxyR orchestrates bacterial oxidative stress response genes in space and time.Cell systems · 2024Article
- Genome reduction improves octanoic acid production in scale down bioreactors.Microbial biotechnology · 2024Article
- Accelerating Genetic Sensor Development, Scale-up, and Deployment Using Synthetic Biology.Biodesign research · 2024Article
- Ribosome profiling reveals the fine-tuned response ofmSystems · 2023Article
- Detecting Photoactivatable Cre-mediated Gene Deletion Efficiency inBio-protocol · 2023Article
- RNAP Promoter Search and Transcription Kinetics in LiveThe journal of physical chemistry. B · 2023Article
- Growth rate-associated transcriptome reorganization in response to genomic, environmental, and evolutionary interruptions.Frontiers in microbiology · 2023Article
- Ozone Disinfection for Elimination of Bacteria and Degradation of SARS-CoV2 RNA for Medical Environments.Genes · 2022Article
- Gene Networks and Pathways Involved inMicroorganisms · 2022Article
Corrections and comments
- Erratum issued
Authors and funding
4 authors at 1 institution in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Environmental perturbations impact multiple cellular traits, including gene expression. Bacteria respond to these stressful situations through complex gene interaction networks, thereby inducing stress tolerance and survival of cells. In this paper, we study the response mechanisms of E. coli when exposed to different environmental stressors via differential expression and co-expression analysis. Gene co-expression networks were generated and analyzed via Weighted Gene Co-expression Network Analysis (WGCNA). Based on the gene co-expression networks, genes with similar expression profiles were clustered into modules. The modules were analysed for identification of hub genes, enrichment of biological processes and transcription factors. In addition, we also studied the link between transcription factors and their differentially regulated targets to understand the regulatory mechanisms involved. These networks validate known gene interactions and provide new insights into genes mediating transcriptional regulation in specific stress environments, thus allowing for in silico hypothesis generation.
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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.