Research article
Rapid and asymmetric divergence of duplicate genes in the human gene coexpression network
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* Corresponding author: Kateryna D Makova kdm16@psu.edu
1 Department of Computer Science and Engineering, Penn State University, University Park, PA, 16802, USA
2 Department of Physics, Penn State University, University Park, PA, 16802, USA
3 Department of Biochemistry and Molecular Biology, Penn State University, University Park, PA, 16802, USA
4 Department of Biology, Penn State University, University Park, PA, 16802, USA
5 Department of Huck Institute for Life Sciences, Penn State University, University Park, PA, 16802, USA
6 Department of Center for Comparative Genomics and Bioinformatics, Penn State University, University Park, PA, 16802, USA
BMC Bioinformatics 2006, 7:46 doi:10.1186/1471-2105-7-46
Published: 27 January 2006Abstract
Background
While gene duplication is known to be one of the most common mechanisms of genome evolution, the fates of genes after duplication are still being debated. In particular, it is presently unknown whether most duplicate genes preserve (or subdivide) the functions of the parental gene or acquire new functions. One aspect of gene function, that is the expression profile in gene coexpression network, has been largely unexplored for duplicate genes.
Results
Here we build a human gene coexpression network using human tissue-specific microarray data and investigate the divergence of duplicate genes in it. The topology of this network is scale-free. Interestingly, our analysis indicates that duplicate genes rapidly lose shared coexpressed partners: after approximately 50 million years since duplication, the two duplicate genes in a pair have only slightly higher number of shared partners as compared with two random singletons. We also show that duplicate gene pairs quickly acquire new coexpressed partners: the average number of partners for a duplicate gene pair is significantly greater than that for a singleton (the latter number can be used as a proxy of the number of partners for a parental singleton gene before duplication). The divergence in gene expression between two duplicates in a pair occurs asymmetrically: one gene usually has more partners than the other one. The network is resilient to both random and degree-based in silico removal of either singletons or duplicate genes. In contrast, the network is especially vulnerable to the removal of highly connected genes when duplicate genes and singletons are considered together.
Conclusion
Duplicate genes rapidly diverge in their expression profiles in the network and play similar role in maintaining the network robustness as compared with singletons.
Contact: kdm16@psu.edu
Supplementary information: Please see additional files.