ArticleProceedings of the National Academy of Sciences of the United States of America2014
Noise decomposition of intracellular biochemical signaling networks using nonequivalent reporters.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 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.
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Who cites it
19 citing papers in PubMed, 41 citations in OpenAlex.
- Assessing the reliability of cellular decision making from noisy, multidimensional single-cell TNF-NF-κB signaling data.PLoS computational biology · 2026Article
- A Neyman-Pearson Framework for Modeling Cellular Decision Making Using Single-Cell TNF-NF-κB Signaling Data.bioRxiv : the preprint server for biology · 2025Article
- Modulating the dynamics of NFκB and PI3K enhances the ensemble-level TNFR1 signaling mediated apoptotic response.NPJ systems biology and applications · 2023Article
- Understanding the physical mechanism of intrinsic noise inside viscous isotropic solids.Scientific reports · 2022Article
- Quantifying information of intracellular signaling: progress with machine learning.Reports on progress in physics. Physical Society (Great Britain) · 2022Review
- Role of integrated noise in pathway-specific signal propagation in feed-forward loops.Theory in biosciences = Theorie in den Biowissenschaften · 2021Article
- Concepts and Applications of Information Theory to Immuno-Oncology.Trends in cancer · 2021Review
- Sensitivity minimization, biological homeostasis and information theory.Biological cybernetics · 2021Review
- Insights about collective decision-making at the genetic level.Biophysical reviews · 2020Article
- Allele-specific single-cell RNA sequencing reveals different architectures of intrinsic and extrinsic gene expression noises.Nucleic acids research · 2020Article
- On Information Extraction and Decoding Mechanisms Improved by Noisy Amplification in Signaling Pathways.Scientific reports · 2019Article
- Noise in the Vertebrate Segmentation Clock Is Boosted by Time Delays but Tamed by Notch Signaling.Cell reports · 2018Article
- Cell-specific responses to the cytokine TGFβ are determined by variability in protein levels.Molecular systems biology · 2018Article
- Universal signal generator for dynamic cell stimulation.Lab on a chip · 2017Article
- Determining the Limitations and Benefits of Noise in Gene Regulation and Signal Transduction through Single Cell, Microscopy-Based Analysis.Journal of molecular biology · 2017Review
- Computation and measurement of cell decision making errors using single cell data.PLoS computational biology · 2017Article
- Distinct cellular states determine calcium signaling response.Molecular systems biology · 2016Article
- Redefining Signaling Pathways with an Expanding Single-Cell Toolbox.Trends in biotechnology · 2016Review
- Information processing in bacteria: memory, computation, and statistical physics: a key issues review.Reports on progress in physics. Physical Society (Great Britain) · 2016Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors at 2 institutions in 1 country.
Funding
Abstract
Experimental measurements of biochemical noise have primarily focused on sources of noise at the gene expression level due to limitations of existing noise decomposition techniques. Here, we introduce a mathematical framework that extends classical extrinsic-intrinsic noise analysis and enables mapping of noise within upstream signaling networks free of such restrictions. The framework applies to systems for which the responses of interest are linearly correlated on average, although the framework can be easily generalized to the nonlinear case. Interestingly, despite the high degree of complexity and nonlinearity of most mammalian signaling networks, three distinct tumor necrosis factor (TNF) signaling network branches displayed linearly correlated responses, in both wild-type and perturbed versions of the network, across multiple orders of magnitude of ligand concentration. Using the noise mapping analysis, we find that the c-Jun N-terminal kinase (JNK) pathway generates higher noise than the NF-κB pathway, whereas the activation of c-Jun adds a greater amount of noise than the activation of ATF-2. In addition, we find that the A20 protein can suppress noise in the activation of ATF-2 by separately inhibiting the TNF receptor complex and JNK pathway through a negative feedback mechanism. These results, easily scalable to larger and more complex networks, pave the way toward assessing how noise propagates through cellular signaling pathways and create a foundation on which we can further investigate the relationship between signaling system architecture and biological noise.
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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.