ArticleGenome research2013
Linking the signaling cascades and dynamic regulatory networks controlling stress responses.
Article in Genome research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 43 papers.
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Who cites it
43 citing papers in PubMed, 84 citations in OpenAlex.
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- Detecting and dissecting signaling crosstalk via the multilayer network integration of signaling and regulatory interactions.Nucleic acids research · 2024Article
- Temporal modelling using single-cell transcriptomics.Nature reviews. Genetics · 2022Review
- The transcriptional response to oxidative stress is independent of stress-granule formation.Molecular biology of the cell · 2022Article
- Reconstructed signaling and regulatory networks identify potential drugs for SARS-CoV-2 infection.bioRxiv : the preprint server for biology · 2021Article
- TSMiner: a novel framework for generating time-specific gene regulatory networks from time-series expression profiles.Nucleic acids research · 2021Article
- Inferring TF activities and activity regulators from gene expression data with constraints from TF perturbation data.Bioinformatics (Oxford, England) · 2021Article
- ViralLink: An integrated workflow to investigate the effect of SARS-CoV-2 on intracellular signalling and regulatory pathways.PLoS computational biology · 2021Article
- Comparative Transcriptomics and Co-Expression Networks Reveal Tissue- and Genotype-Specific Responses ofGenes · 2020Article
- NetConfer: a web application for comparative analysis of multiple biological networks.BMC biology · 2020Article
- Inferring signalling dynamics by integrating interventional with observational data.Bioinformatics (Oxford, England) · 2019Article
- Protein interaction disruption in cancer.BMC cancer · 2019Article
- REFINING CELLULAR PATHWAY MODELS USING AN ENSEMBLE OF HETEROGENEOUS DATA SOURCES.The annals of applied statistics · 2018Article
- Archetypal transcriptional blocks underpin yeast gene regulation in response to changes in growth conditions.Scientific reports · 2018Article
- iDREM: Interactive visualization of dynamic regulatory networks.PLoS computational biology · 2018Article
- Article
- Reconstructing cancer drug response networks using multitask learning.BMC systems biology · 2017Article
- An Integrative Framework Reveals Signaling-to-Transcription Events in Toll-like Receptor Signaling.Cell reports · 2017Article
- Integrated systems biology analysis of KSHV latent infection reveals viral induction and reliance on peroxisome mediated lipid metabolism.PLoS pathogens · 2017Article
- Article
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 2 countries.
Funding
Abstract
Accurate models of the cross-talk between signaling pathways and transcriptional regulatory networks within cells are essential to understand complex response programs. We present a new computational method that combines condition-specific time-series expression data with general protein interaction data to reconstruct dynamic and causal stress response networks. These networks characterize the pathways involved in the response, their time of activation, and the affected genes. The signaling and regulatory components of our networks are linked via a set of common transcription factors that serve as targets in the signaling network and as regulators of the transcriptional response network. Detailed case studies of stress responses in budding yeast demonstrate the predictive power of our method. Our method correctly identifies the core signaling proteins and transcription factors of the response programs. It further predicts the involvement of additional transcription factors and other proteins not previously implicated in the response pathways. We experimentally verify several of these predictions for the osmotic stress response network. Our approach requires little condition-specific data: only a partial set of upstream initiators and time-series gene expression data, which are readily available for many conditions and species. Consequently, our method is widely applicable and can be used to derive accurate, dynamic response models in several species.
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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.