ArticleProceedings of the National Academy of Sciences of the United States of America2006
Transcriptional response of steady-state yeast cultures to transient perturbations in carbon source.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 48 papers.
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Who cites it
48 citing papers in PubMed, 97 citations in OpenAlex.
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- Is heterogeneity in large-scale bioreactors a real problem in recombinant protein synthesis by Pichia pastoris?Applied microbiology and biotechnology · 2023Article
- The metabolite-controlled ubiquitin conjugase Ubc8 promotes mitochondrial protein import.Life science alliance · 2023Article
- Fluctuating Environments Maintain Genetic Diversity through Neutral Fitness Effects and Balancing Selection.Molecular biology and evolution · 2021Article
- Inferring TF activities and activity regulators from gene expression data with constraints from TF perturbation data.Bioinformatics (Oxford, England) · 2021Article
- Molecular signatures of aneuploidy-driven adaptive evolution.Nature communications · 2020Article
- A fast and tuneable auxin-inducible degron for depletion of target proteins in budding yeast.Yeast (Chichester, England) · 2019Article
- Quantitative Flow Cytometry to Understand Population Heterogeneity in Response to Changes in Substrate Availability inFrontiers in bioengineering and biotechnology · 2019Article
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- Steady-state and dynamic gene expression programs in Saccharomyces cerevisiae in response to variation in environmental nitrogen.Molecular biology of the cell · 2016Article
- OM-FBA: Integrate Transcriptomics Data with Flux Balance Analysis to Decipher the Cell Metabolism.PloS one · 2016Article
- Functional Analysis and Characterization of Differential Coexpression Networks.Scientific reports · 2015Article
- Contribution of Sequence Motif, Chromatin State, and DNA Structure Features to Predictive Models of Transcription Factor Binding in Yeast.PLoS computational biology · 2015Article
- Timing and Variability of Galactose Metabolic Gene Activation Depend on the Rate of Environmental Change.PLoS computational biology · 2015Article
- How to train your microbe: methods for dynamically characterizing gene networks.Current opinion in microbiology · 2015Review
- A hybrid imputation approach for microarray missing value estimation.BMC genomics · 2015Article
- Bicluster Sampled Coherence Metric (BSCM) provides an accurate environmental context for phenotype predictions.BMC systems biology · 2015Article
- Functional characterization of a Penicillium chrysogenum mutanase gene induced upon co-cultivation with Bacillus subtilis.BMC microbiology · 2014Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 2 countries.
Funding
Abstract
To understand the dynamics of transcriptional response to changing environments, well defined, easily controlled, and short-term perturbation experiments were undertaken. We subjected steady-state cultures of Saccharomyces cerevisiae in chemostats growing on limiting galactose to two different size pulses of glucose, well known to be a preferred carbon source. Although these pulses were not large enough to change growth rates or cell size, approximately 25% of the genes changed their expression at least 2-fold. Using DNA microarrays to estimate mRNA abundance, we found a number of distinguishable patterns of transcriptional response among the many genes whose expression changed. Many of these genes were already known to be regulated by particular transcription factors; we estimated five potentially relevant transcription factor activities from the observed changes in gene expression (i.e., Mig1p, Gal4p, Cat8p, Rgt1p, Adr1p, and Rcs1p). With these estimates, for two regulatory circuits involving interaction among multiple regulators we could generate dynamical models that quantitatively account for the observed transcriptional responses to the transient perturbations.
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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.