ArticleIET systems biology2008
Proximity of intracellular regulatory networks to monotone systems.
Article in IET systems biology, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 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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Who cites it
13 citing papers in PubMed, 44 citations in OpenAlex.
- Minimal frustration underlies the usefulness of incomplete regulatory network models in biology.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
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- Discovering design principles for biological functionalities:Perspectives from systems biology.Journal of biosciences · 2022Review
- An evolutionary game approach for determination of the structural conflicts in signed networks.Scientific reports · 2016Article
- Early phase of plasticity-related gene regulation and SRF dependent transcription in the hippocampus.PloS one · 2013Article
- Novel factors in the pathogenesis of psoriasis and potential drug candidates are found with systems biology approach.PloS one · 2013Article
- Article
- Trafficking motifs as the basis for two-compartment signaling systems to form multiple stable states.Biophysical journal · 2011Article
- Elementary signaling modes predict the essentiality of signal transduction network components.BMC systems biology · 2011Article
- Monotonicity, frustration, and ordered response: an analysis of the energy landscape of perturbed large-scale biological networks.BMC systems biology · 2010Article
- Inferring the Sign of Kinase-Substrate Interactions by Combining Quantitative Phosphoproteomics with a Literature-Based Mammalian Kinome Network.Proceedings. IEEE International Symposium on Bioinformatics and Bioengineering · 2010Article
- Network-free inference of knockout effects in yeast.PLoS computational biology · 2010Article
- Insights into the organization of biochemical regulatory networks using graph theory analyses.The Journal of biological chemistry · 2009Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors at 2 institutions in 1 country.
Funding
Abstract
Networks that contain only sign-consistent loops, such as positive feedforward and feedback loops, function as monotone systems. Simulated using differential equations, monotone systems display well-ordered behaviour that excludes the possibility for chaotic dynamics. Perturbations of such systems have unambiguous global effects and a predictability characteristic that confers robustness and adaptability. The authors assess whether the topology of biological regulatory networks is similar to the topology of monotone systems. For this, three intracellular regulatory networks are analysed where links are specified for the directionality and the effects of interactions. These networks were assembled from functional studies in the experimental literature. It is found that the three biological networks contain far more positive 'sign-consistent' feedback and feedforward loops than negative loops. Negative loops can be 'eliminated' from the real networks by the removal of fewer links as compared with the corresponding shuffled networks. The abundance of positive feedforward and feedback loops in real networks emerges from the presence of hubs that are enriched with either negative or positive links. These observations suggest that intracellular regulatory networks are 'close-to-monotone', a characteristic that could contribute to the dynamical stability observed in cellular behaviour.
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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.