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The yeast coexpression network has a small-world, scale-free architecture and can be explained by a simple model
Vera van Noort1, Berend Snel, Martijn A Huynen
1Nijmegen Center for Molecular Life Sciences, P/A Center for Molecular and Biomolecular Informatics, Nijmegen, The Netherlands.
EMBO Reports
|February 18, 2004
Summary
We developed a new model for gene coexpression network evolution in yeast. This model explains the observed scale-free, small-world architecture and gene homology without invoking selection.
Area of Science:
- Systems biology
- Computational biology
- Genomics
Background:
- Gene coexpression networks in Saccharomyces cerevisiae exhibit scale-free, small-world architecture.
- Existing models fail to fully explain the evolutionary origins of these intracellular network features.
Purpose of the Study:
- To derive a novel evolutionary model for gene coexpression networks.
- To explain the observed network architecture and homology relationships.
Main Methods:
- Investigated gene coexpression in Saccharomyces cerevisiae.
- Developed a neutralist's model incorporating gene/TFBS duplication, TFBS modification, and gene loss.
- Linked genes sharing multiple transcription factor binding sites (TFBSs).
Main Results:
- The proposed model successfully reproduces the scale-free, small-world architecture of the yeast coexpression network.
- The model also explains homology relations between coregulated genes.
- No selection at the network or gene regulation level was required.
Conclusions:
- A simple, neutralist's model adequately explains the evolution of gene coexpression networks.
- The model highlights the importance of TFBS dynamics and gene duplication in shaping biological networks.