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Published on: December 7, 2021
Evolutionary conservation and over-representation of functionally enriched network patterns in the yeast regulatory
Ofer Meshi1, Tomer Shlomi, Eytan Ruppin
1School of Computer Science, Tel-Aviv University, Tel-Aviv, Israel. meshi@post.tau.ac.il
BMC Systems Biology
|April 6, 2007
Summary
Network patterns in yeast regulatory networks are functionally significant, but over-representation doesn't identify them. Recent gene evolution, not conservation, links to function, challenging motif detection methods.
Area of Science:
- Systems biology
- Bioinformatics
- Genomics
Background:
- Biological networks often exhibit localized patterns assumed to reflect optimal design.
- Network motifs, identified by over-representation, are commonly used to find functional components.
- Recent studies question the functional significance and optimal design principles of over-represented network patterns.
Purpose of the Study:
- To investigate the functional significance of regulatory network patterns.
- To evaluate the role of biological annotation and evolutionary conservation in understanding network patterns.
- To assess the suitability of over-representation methods for identifying functionally important network patterns.
Main Methods:
- Enumeration of all 3-node network patterns in the yeast Saccharomyces cerevisiae regulatory network.
- Analysis of Gene Ontology (GO) annotation for genes within these patterns.
- Assessment of evolutionary conservation of genes constituting different network patterns.
Main Results:
- Specific 3-node network patterns show functional enrichment under various cellular conditions.
- Functionally enriched patterns are primarily composed of recently evolved genes.
- No correlation was observed between network pattern over-representation and functional enrichment.
Conclusions:
- Functional enrichment supports network patterns as a key design principle in regulatory networks.
- The standard method of over-representation is inadequate for detecting functionally enriched patterns.
- Evolutionary conservation does not appear to be a driving force for preserving functionally enriched network patterns.
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