ArticleCell systems2017
Iterative Modeling Reveals Evidence of Sequential Transcriptional Control Mechanisms.
Article in Cell systems, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
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
37 citing papers in PubMed, 49 citations in OpenAlex.
- Rising from the fragments: a multi-factorial regulatory framework of DNA damage response in Deinococcus radiodurans.Extremophiles : life under extreme conditions · 2026Review
- Review
- Post-transcriptional regulatory networks: The dynamic interplay of RNA-binding proteins.The FEBS journal · 2026Review
- Decoding cellular population dynamics through mechanistic modelling and statistical data analysis.NPJ systems biology and applications · 2026Review
- JNK activation dynamics drive distinct gene expression patterns over time mediated by mRNA stability.NPJ systems biology and applications · 2025Article
- Gene regulatory logic of the interferon-β enhancer is characterized by two selectively deployed modes of transcription factor synergy.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Synergy and antagonism in the integration of BCR and CD40 signals that control B-cell population expansion.Molecular systems biology · 2025Article
- NF-κB: master regulator of cellular responses in health and disease.Immunity & inflammation · 2025Review
- Single-cell stimulus-response gene expression trajectories reveal the stimulus specificities of dynamic responses by single macrophages.Molecular cell · 2024Article
- Dynamical and combinatorial coding by MAPK p38 and NFκB in the inflammatory response of macrophages.Molecular systems biology · 2024Article
- Detecting and dissecting signaling crosstalk via the multilayer network integration of signaling and regulatory interactions.Nucleic acids research · 2024Article
- RelB-deficient autoinflammatory pathology presents as interferonopathy, but in mice is interferon-independent.The Journal of allergy and clinical immunology · 2023Article
- Tonic TNF conditioning of macrophages safeguards stimulus-specific inflammatory responses.EMBO reports · 2023Article
- Quantifying stimulus-response specificity to probe the functional state of macrophages.Cell systems · 2023Article
- The tempo and mode of gene regulatory programs during bacterial infection.Cell reports · 2022Article
- Functional Hallmarks of Healthy Macrophage Responses: Their Regulatory Basis and Disease Relevance.Annual review of immunology · 2022Review
- Controlling Cancer Cell Death Types to Optimize Anti-Tumor Immunity.Biomedicines · 2022Review
- Pathogenic TNF-α drives peripheral nerve inflammation in an Aire-deficient model of autoimmunity.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Review
- NF-κB dynamics determine the stimulus specificity of epigenomic reprogramming in macrophages.Science (New York, N.Y.) · 2021Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors at 2 institutions in 1 country.
Funding
Abstract
Combinatorial control of gene expression is presumed to be mediated by molecular interactions between coincident transcription factors (TFs). While information on the genome-wide locations of TFs is available, the genes they regulate and whether they function combinatorially often remain open questions. Here, we developed a mechanistic, rather than statistical, modeling approach to elucidate TF control logic from gene expression data. Applying this approach to hundreds of genes in 85 datasets measuring the transcriptional responses of murine fibroblasts and macrophages to cytokines and pathogens, we found that stimulus-responsive TFs generally function sequentially in logical OR gates or singly. Logical AND gates were found between NF-κB-responsive mRNA synthesis and MAPKp38-responsive control of mRNA half-life, but not between temporally coincident TFs. Our analyses identified the functional target genes of each of the pathogen-responsive TFs and prompt a revision of the conceptual underpinnings of combinatorial control of gene expression to include sequentially acting molecular mechanisms that govern mRNA synthesis and decay.
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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.