ArticleGenome research2005
A network of transcriptionally coordinated functional modules in Saccharomyces cerevisiae.
Article in Genome research, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- A novel statistical approach for identification of the master regulator transcription factor.BMC bioinformatics · 2017Article
- Feature Identification of Compensatory Gene Pairs without Sequence Homology in Yeast.Comparative and functional genomics · 2012Article
- Extracting regulatory modules from gene expression data by sequential pattern mining.BMC genomics · 2011Article
- Dynamic gene network reconstruction from gene expression data in mice after influenza A (H1N1) infection.Journal of clinical bioinformatics · 2011Article
- A novel method to identify cooperative functional modules: study of module coordination in the Saccharomyces cerevisiae cell cycle.BMC bioinformatics · 2011Article
- Composite functional module inference: detecting cooperation between transcriptional regulation and protein interaction by mantel test.BMC systems biology · 2010Article
- Detecting coordinated regulation of multi-protein complexes using logic analysis of gene expression.BMC systems biology · 2009Article
- Modeling and characterization of disease associated subnetworks in the human interactome using machine learning.Summit on translational bioinformatics · 2009Article
- Investigating topological and functional features of multimodular proteins.Journal of biomedicine & biotechnology · 2009Article
- Gene module level analysis: identification to networks and dynamics.Current opinion in biotechnology · 2008Review
- Validating module network learning algorithms using simulated data.BMC bioinformatics · 2007Article
- Modularity and dynamics of cellular networks.PLoS computational biology · 2006Review
- A literature-based similarity metric for biological processes.BMC bioinformatics · 2006Article
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Authors and funding
2 authors.
Funding
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Abstract
Recent computational and experimental work suggests that functional modules underlie much of cellular physiology and are a useful unit of cellular organization from the perspective of systems biology. Because interactions among modules can give rise to higher-level properties that are essential to cellular function, a complete knowledge of these interactions is necessary for future work in systems biology, including in silico modeling and metabolic engineering. Here we present a computational method for the systematic identification and analysis of functional modules whose activity is coordinated at the level of transcription. We applied this method, Search for Pairwise Interactions (SPIN), to obtain a global view of functional module connectivity in Saccharomyces cerevisiae and to provide insight into the biological mechanisms underlying this coordination. We also examined this global network at higher resolution to obtain detailed information about the interactions of particular module pairs. For instance, our results reveal possible transcriptional coordination of glycolysis and lipid metabolism by the transcription factor Gcr1p, and further suggest that glycolysis and phosphoinositide signaling may regulate each other reciprocally.
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