ArticleNPJ systems biology and applications2015
Network reconstruction and validation of the Snf1/AMPK pathway in baker's yeast based on a comprehensive literature review.
Article in NPJ systems biology and applications, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed, 27 citations in OpenAlex.
- Engineering ATP Import in Yeast Uncovers a Synthetic Route to Extend Cellular Lifespan.bioRxiv : the preprint server for biology · 2025Article
- The small GTPase Rho5-Yet another player in yeast glucose signaling.PLoS genetics · 2025Article
- Data integration strategies for whole-cell modeling.FEMS yeast research · 2024Review
- A detailed molecular network map and model of the NLRP3 inflammasome.Frontiers in immunology · 2023Review
- Multi-scale model suggests the trade-off between protein and ATP demand as a driver of metabolic changes during yeast replicative ageing.PLoS computational biology · 2022Article
- Modelling of glucose repression signalling in yeast Saccharomyces cerevisiae.FEMS yeast research · 2022Review
- D-Xylose Sensing inInternational journal of molecular sciences · 2021Review
- An abscisic acid-responsive protein interaction network for sucrose non-fermenting related kinase1 in abiotic stress response.Communications biology · 2020Article
- A scalable method for parameter-free simulation and validation of mechanistic cellular signal transduction network models.NPJ systems biology and applications · 2020Article
- Snf1 cooperates with the CWI MAPK pathway to mediate the degradation of Med13 following oxidative stress.Microbial cell (Graz, Austria) · 2018Article
- Robustness of Nutrient Signaling Is Maintained by Interconnectivity Between Signal Transduction Pathways.Frontiers in physiology · 2018Article
Corrections and comments
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Authors and funding
7 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
BACKGROUND/
objectivesThe SNF1/AMPK protein kinase has a central role in energy homeostasis in eukaryotic cells. It is activated by energy depletion and stimulates processes leading to the production of ATP while it downregulates ATP-consuming processes. The yeast SNF1 complex is best known for its role in glucose derepression.
methodsWe performed a network reconstruction of the Snf1 pathway based on a comprehensive literature review. The network was formalised in the rxncon language, and we used the rxncon toolbox for model validation and gap filling.
resultsWe present a machine-readable network definition that summarises the mechanistic knowledge of the Snf1 pathway. Furthermore, we used the known input/output relationships in the network to identify and fill gaps in the information transfer through the pathway, to produce a functional network model. Finally, we convert the functional network model into a rule-based model as a proof-of-principle.
conclusionsThe workflow presented here enables large scale reconstruction, validation and gap filling of signal transduction networks. It is analogous to but distinct from that established for metabolic networks. We demonstrate the workflow capabilities, and the direct link between the reconstruction and dynamic modelling, with the Snf1 network. This network is a distillation of the knowledge from all previous publications on the Snf1/AMPK pathway. The network is a knowledge resource for modellers and experimentalists alike, and a template for similar efforts in higher eukaryotes. Finally, we envisage the workflow as an instrumental tool for reconstruction of large signalling networks across Eukaryota.
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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.