Int. J. Mol. Sci. 2009, 10(8), 3658-3670; doi:10.3390/ijms10083658
Article

Co-Expression of Neighboring Genes in the Zebrafish (Danio rerio) Genome

1 Institute of Information Science, Academia Sinica, 128 Sec. 2, Academia Rd, Nankang, 115, Taipei, Taiwan 2 Department of Computer Science and Information Engineering, National Taiwan University, Taipei 106, Taiwan 3 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
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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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MDPI and ACS Style

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.

AMA Style

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.

Chicago/Turabian Style

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.

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