ArticleGenome research2003
Reconciling gene expression data with known genome-scale regulatory network structures.
Article in Genome research, 2003. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers.
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Who cites it
40 citing papers in PubMed.
- Differences in evolutionary accessibility determine which equally effective regulatory motif evolves to generate pulses.Genetics · 2021Article
- E. coli gene regulatory networks are inconsistent with gene expression data.Nucleic acids research · 2019Article
- Detection of network motifs using three-way ANOVA.PloS one · 2018Article
- Gaussian graphical model for identifying significantly responsive regulatory networks from time course high-throughput data.IET systems biology · 2013Article
- An approach for dynamical network reconstruction of simple network motifs.BMC systems biology · 2013Article
- One Hand Clapping: detection of condition-specific transcription factor interactions from genome-wide gene activity data.Nucleic acids research · 2012Article
- Optimality principles in the regulation of metabolic networks.Metabolites · 2012Article
- Learning transcriptional regulation on a genome scale: a theoretical analysis based on gene expression data.Briefings in bioinformatics · 2012Review
- Towards an evolutionary model of transcription networks.PLoS computational biology · 2011Article
- BN+1 Bayesian network expansion for identifying molecular pathway elements.Communicative & integrative biology · 2010Article
- Article
- Advantages and limitations of current network inference methods.Nature reviews. Microbiology · 2010Review
- Patterns of subnet usage reveal distinct scales of regulation in the transcriptional regulatory network of Escherichia coli.PLoS computational biology · 2010Article
- Module network inference from a cancer gene expression data set identifies microRNA regulated modules.PloS one · 2010Article
- Article
- Ranges of control in the transcriptional regulation of Escherichia coli.BMC systems biology · 2009Article
- Mechanisms and evolution of control logic in prokaryotic transcriptional regulation.Microbiology and molecular biology reviews : MMBR · 2009Review
- Comparative analysis of module-based versus direct methods for reverse-engineering transcriptional regulatory networks.BMC systems biology · 2009Article
- Exploring pathways from gene co-expression to network dynamics.Methods in molecular biology (Clifton, N.J.) · 2009Review
- Principles of transcriptional regulation and evolution of the metabolic system in E. coli.Genome research · 2009Article
Corrections and comments
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Authors and funding
3 authors.
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Abstract
The availability of genome-scale gene expression data sets has initiated the development of methods that use this data to infer transcriptional regulatory networks. Alternatively, such regulatory network structures can be reconstructed based on annotated genome information, well-curated databases, and primary research literature. As a first step toward reconciling the two approaches, we examine the consistency between known genome-wide regulatory network structures and extensive gene expression data collections in Escherichia coli and Saccharomyces cerevisiae. By decomposing the regulatory network into a set of basic network elements, we can compute the local consistency of each instance of a particular type of network element. We find that the consistency of network elements is influenced by both structural features of the network such as the number of regulators acting on a target gene and by the functional classes of the genes involved in a particular element. Taken together, the approach presented allows us to define regulatory network subcomponents with a high degree of consistency between the network structure and gene expression data. The results suggest that targeted gene expression profiling data can be used to refine and expand particular subcomponents of known regulatory networks that are sufficiently decoupled from the rest of the network.
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