Int. J. Mol. Sci. 2009, 10(1), 116-132; doi:10.3390/ijms10010116
Article

Function Annotation of an SBP-box Gene in Arabidopsis Based on Analysis of Co-expression Networks and Promoters

Yi Wang 1 email, Zongli Hu 1 email, Yuxin Yang 1 email, Xuqing Chen 1,2 email and Guoping Chen 1,* email
1 College of Bioengineering, Chongqing University, Chongqing 400030, P.R. China 2 Beijing Research Center of Agro-Biotechnology, Beijing 100089, P.R.China
* Author to whom correspondence should be addressed.
Received: 21 October 2008; in revised form: 15 December 2008 / Accepted: 18 December 2008 / Published: 2 January 2009
(This article belongs to the Special Issue Algorithms and Molecular Sciences)
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Abstract: The SQUAMOSA PROMOTER BINDING PROTEIN–LIKE (SPL) gene family is an SBP-box transcription family in Arabidopsis. While several physiological responses to SPL genes have been reported, their biological role remains elusive. Here, we use a combined analysis of expression correlation, the interactome, and promoter content to infer the biological role of the SPL genes in Arabidopsis thaliana. Analysis of the SPL-correlated gene network reveals multiple functions for SPL genes. Network analysis shows that SPL genes function by controlling other transcription factor families and have relatives with membrane protein transport activity. The interactome analysis of the correlation genes suggests that SPL genes also take part in metabolism of glucose, inorganic salts, and ATP production. Furthermore, the promoters of the correlated genes contain a core binding cis-element (GTAC). All of these analyses suggest that SPL genes have varied functions in Arabidopsis.
Keywords: Arabidopsis; SPL; co-expression; network; promoter

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MDPI and ACS Style

Wang, Y.; Hu, Z.; Yang, Y.; Chen, X.; Chen, G. Function Annotation of an SBP-box Gene in Arabidopsis Based on Analysis of Co-expression Networks and Promoters. Int. J. Mol. Sci. 2009, 10, 116-132.

AMA Style

Wang Y, Hu Z, Yang Y, Chen X, Chen G. Function Annotation of an SBP-box Gene in Arabidopsis Based on Analysis of Co-expression Networks and Promoters. International Journal of Molecular Sciences. 2009; 10(1):116-132.

Chicago/Turabian Style

Wang, Yi; Hu, Zongli; Yang, Yuxin; Chen, Xuqing; Chen, Guoping. 2009. "Function Annotation of an SBP-box Gene in Arabidopsis Based on Analysis of Co-expression Networks and Promoters." Int. J. Mol. Sci. 10, no. 1: 116-132.

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