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Co-Expression of Neighboring Genes in the Zebrafish (Danio rerio) Genome
Institute of Information Science, Academia Sinica, 128 Sec. 2, Academia Rd, Nankang, 115, Taipei, Taiwan
Department of Computer Science and Information Engineering, National Taiwan University, Taipei 106, Taiwan
Biodiversity Research Center, Academia Sinica, 128 Sec. 2, Academia Rd, Nankang, 115, Taipei, Taiwan
* Author to whom correspondence should be addressed.
Received: 14 July 2009; in revised form: 11 August 2009 / Accepted: 20 August 2009 / Published: 21 August 2009
Abstract: Neighboring genes in the eukaryotic genome have a tendency to express concurrently, and the proximity of two adjacent genes is often considered a possible explanation for their co-expression behavior. However, the actual contribution of the physical distance between two genes to their co-expression behavior has yet to be defined. To further investigate this issue, we studied the co-expression of neighboring genes in zebrafish, which has a compact genome and has experienced a whole genome duplication event. Our analysis shows that the proportion of highly co-expressed neighboring pairs (Pearson’s correlation coefficient R>0.7) is low (0.24% ~ 0.67%); however, it is still significantly higher than that of random pairs. In particular, the statistical result implies that the co-expression tendency of neighboring pairs is negatively correlated with their physical distance. Our findings therefore suggest that physical distance may play an important role in the co-expression of neighboring genes. Possible mechanisms related to the neighboring genes’ co-expression are also discussed.
Keywords: gene expression; co-expression; neighboring genes; promoter; zebrafish
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Tsai, H.-K.; Huang, P.-Y.; Kao, C.-Y.; Wang, D. Co-Expression of Neighboring Genes in the Zebrafish (Danio rerio) Genome. Int. J. Mol. Sci. 2009, 10, 3658-3670.
Tsai H-K, Huang P-Y, Kao C-Y, Wang D. Co-Expression of Neighboring Genes in the Zebrafish (Danio rerio) Genome. International Journal of Molecular Sciences. 2009; 10(8):3658-3670.
Tsai, Huai-Kuang; Huang, Pei-Ying; Kao, Cheng-Yan; Wang, Daryi. 2009. "Co-Expression of Neighboring Genes in the Zebrafish (Danio rerio) Genome." Int. J. Mol. Sci. 10, no. 8: 3658-3670.