ArticleMolecular systems biology2009
Elucidating regulatory mechanisms downstream of a signaling pathway using informative experiments.
Article in Molecular systems biology, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Probing transcription factor subsets in gene regulatory networks.Algorithms for molecular biology : AMB · 2026Article
- Global quantitative understanding of non-equilibrium cell fate decision-making in response to pheromone.iScience · 2023Article
- Learning signaling networks from combinatorial perturbations by exploiting siRNA off-target effects.Bioinformatics (Oxford, England) · 2019Article
- CrossPlan: systematic planning of genetic crosses to validate mathematical models.Bioinformatics (Oxford, England) · 2018Article
- A review of active learning approaches to experimental design for uncovering biological networks.PLoS computational biology · 2017Review
- Linear effects models of signaling pathways from combinatorial perturbation data.Bioinformatics (Oxford, England) · 2016Article
- Translation of Genotype to Phenotype by a Hierarchy of Cell Subsystems.Cell systems · 2016Article
- Designing Experiments to Discriminate Families of Logic Models.Frontiers in bioengineering and biotechnology · 2015Article
- Experimental design schemes for learning Boolean network models.Bioinformatics (Oxford, England) · 2014Article
- Bioinformatics and computational biology in Poland.PLoS computational biology · 2013Article
- Computationally Driven Experimental Biology.Computer · 2012Article
- Deregulation upon DNA damage revealed by joint analysis of context-specific perturbation data.BMC bioinformatics · 2011Article
- Towards genome-scale signalling network reconstructions.Nature reviews. Genetics · 2010Review
- How to understand the cell by breaking it: network analysis of gene perturbation screens.PLoS computational biology · 2010Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Signaling cascades are triggered by environmental stimulation and propagate the signal to regulate transcription. Systematic reconstruction of the underlying regulatory mechanisms requires pathway-targeted, informative experimental data. However, practical experimental design approaches are still in their infancy. Here, we propose a framework that iterates design of experiments and identification of regulatory relationships downstream of a given pathway. The experimental design component, called MEED, aims to minimize the amount of laboratory effort required in this process. To avoid ambiguity in the identification of regulatory relationships, the choice of experiments maximizes diversity between expression profiles of genes regulated through different mechanisms. The framework takes advantage of expert knowledge about the pathways under study, formalized in a predictive logical model. By considering model-predicted dependencies between experiments, MEED is able to suggest a whole set of experiments that can be carried out simultaneously. Our framework was applied to investigate interconnected signaling pathways in yeast. In comparison with other approaches, MEED suggested the most informative experiments for unambiguous identification of transcriptional regulation in this system.
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