ArticleNature communications2024
Proteome allocation is linked to transcriptional regulation through a modularized transcriptome.
Article in Nature communications, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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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.
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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.
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Who cites it
10 citing papers in PubMed.
- iModulonMiner 2.0: multi-modality modularization of prokaryotic bulk, single-cell, and community omics data.Nucleic acids research · 2026Article
- Review
- Integrated network pharmacology, transcriptomics and proteomics unveils the mechanisms of Forsythiae Fructus against acute lung injury.Die Naturwissenschaften · 2026Article
- Aerobicity stimulon iniScience · 2026Article
- Human body temperature cues widespread changes in virulence gene expression in uropathogenicInfection and immunity · 2026Article
- Proteome-Wide Analysis and Surface Protein Isolation for Secretome Characterization Reveal Insights into the Biology of the Leaf-Cutter AntAnalytical chemistry · 2025Article
- Transcriptional regulatory networks of the human gut symbiont Bacteroides thetaiotaomicron are uncovered using machine learning.Nucleic acids research · 2025Article
- Gene network centrality analysis identifies key regulators coordinating day-night metabolic transitions inFrontiers in microbiology · 2025Article
- The hallmarks of a tradeoff in transcriptomes that balances stress and growth functions.mSystems · 2024Article
- The hallmarks of a tradeoff in transcriptomes that balances stress and growth functions.Research square · 2023Article
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Authors and funding
9 authors.
Funding
Abstract
It has proved challenging to quantitatively relate the proteome to the transcriptome on a per-gene basis. Recent advances in data analytics have enabled a biologically meaningful modularization of the bacterial transcriptome. We thus investigate whether matched datasets of transcriptomes and proteomes from bacteria under diverse conditions can be modularized in the same way to reveal novel relationships between their compositions. We find that; (1) the modules of the proteome and the transcriptome are comprised of a similar list of gene products, (2) the modules in the proteome often represent combinations of modules from the transcriptome, (3) known transcriptional and post-translational regulation is reflected in differences between two sets of modules, allowing for knowledge-mapping when interpreting module functions, and (4) through statistical modeling, absolute proteome allocation can be inferred from the transcriptome alone. Quantitative and knowledge-based relationships can thus be found at the genome-scale between the proteome and transcriptome in bacteria.
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