The DOI matches its Crossref record; 7 of the 7 references it cites were found in a registry or an index.
Integrated analysis of regulatory and metabolic networks reveals novel regulatory mechanisms in Saccharomyces cerevisiae
Open accessAbstract
We describe the use of model-driven analysis of multiple data types relevant to transcriptional regulation of metabolism to discover novel regulatory mechanisms in Saccharomyces cerevisiae. We have reconstructed the nutrient-controlled transcriptional regulatory network controlling metabolism in S. cerevisiae consisting of 55 transcription factors regulating 750 metabolic genes, based on information in the primary literature. This reconstructed regulatory network coupled with an existing genome-scale metabolic network model allows in silico prediction of growth phenotypes of regulatory gene deletions as well as gene expression profiles. We compared model predictions of gene expression changes in response to genetic and environmental perturbations to experimental data to identify potential novel targets for transcription factors. We then identified regulatory cascades connecting transcription factors to the potential targets through a systematic model expansion strategy using published genome-wide chromatin immunoprecipitation and binding-site-motif data sets. Finally, we show the ability of an integrated metabolic and regulatory network model to predict growth phenotypes of transcription factor knockout strains. These studies illustrate the potential of model-driven data integration to systematically discover novel components and interactions in regulatory and metabolic networks in eukaryotic cells.
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Genomic Expression Programs in the Response of Yeast Cells to Environmental Changes
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Functional Characterization of the S. cerevisiae Genome by Gene Deletion and Parallel Analysis
Winzeler, E. A., Shoemaker, D. D., Astromoff, A., Liang, H., Anderson, K., Andre, B., Bangham, R., Benito, R., Boeke, J. D., Bussey, H., et al. (1999) · Science · doi:10.1126/science.285.5429.901 · Cited by 3,953
Calorie restriction extends Saccharomyces cerevisiae lifespan by increasing respiration
Lin, S.-J., Kaeberlein, M., Andalis, A. A., Sturtz, L. A., Defossez, P.-A., Culotta, V. C., Fink, G. R., & Guarente, L. (2002) · Nature · doi:10.1038/nature00829 · Cited by 1,057
Integrating high-throughput and computational data elucidates bacterial networks
Covert, M. W., Knight, E. M., Reed, J. L., Herrgard, M. J., & Palsson, B. O. (2004) · Nature · doi:10.1038/nature02456 · Cited by 792
Self-citationFamili, I., Förster, J., Nielsen, J., & Palsson, B. O. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2235812100 · Cited by 353
Self-citationEffect of Specific Growth Rate on Fermentative Capacity of Baker’s Yeast
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Cited by
Modelling and analysis of gene regulatory networks
Karlebach, G., & Shamir, R. (2008) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm2503 · Cited by 1,296
Applications of genome‐scale metabolic reconstructions
Oberhardt, M. A., Palsson, B. Ø., & Papin, J. A. (2009) · Molecular Systems Biology · doi:10.1038/msb.2009.77 · Cited by 828
Self-citationConstraining the metabolic genotype–phenotype relationship using a phylogeny of in silico methods
Lewis, N. E., Nagarajan, H., & Palsson, B. O. (2012) · Nature Reviews Microbiology · doi:10.1038/nrmicro2737 · Cited by 779
Self-citationIntegrative approaches for finding modular structure in biological networks
Mitra, K., Carvunis, A.-R., Ramesh, S. K., & Ideker, T. (2013) · Nature Reviews Genetics · doi:10.1038/nrg3552 · Cited by 535
Flux balance analysis of biological systems: applications and challenges
Raman, K., & Chandra, N. (2009) · Briefings in Bioinformatics · doi:10.1093/bib/bbp011 · Cited by 437
Metadata
- Authors
- Herrgård, M. J., Lee, B.-S., Portnoy, V., & Palsson, B. Ø.
- Venue
- Genome Research
- Publisher
- Cold Spring Harbor Laboratory
- Published
- 2006-04-10
- Volume
- 16
- Issue
- 5
- Pages
- 627-635
- ISSN
- 1088-9051 (ISSN-L)
- OpenAlex
- W2002880495
- Cited by
- 223
- References
- 7
- Type
- posted content
- Language
- en
- Open access
- bronze
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- Herrgård, M. J., Lee, B.-S., Portnoy, V., & Palsson, B. Ø. (2006). Integrated analysis of regulatory and metabolic networks reveals novel regulatory mechanisms in Saccharomyces cerevisiae. Genome Research. https://doi.org/10.1101/gr.4083206
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Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
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