Next Article in Journal
Compensatory Growth Induced in Zebrafish Larvae after Pre-Exposure to a Microcystis aeruginosa Natural Bloom Extract Containing Microcystins
Next Article in Special Issue
On the Reconstruction of Three-dimensional Protein Structures from Contact Maps
Previous Article in Journal
An Overview of Conventional and Emerging Analytical Methods for the Determination of Mycotoxins
Previous Article in Special Issue
Hierarchical Clustering of Large Databases and Classification of Antibiotics at High Noise Levels
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

1
, 1
, 1
, 1,2
 and 1,*
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)
View Full-Text   |   Download PDF [732 KB, uploaded 19 June 2014]   |   Browse Figures
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 Arabidopsis; SPL; co-expression; network; promoter
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Export to BibTeX |
EndNote


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.


Int. J. Mol. Sci. EISSN 1422-0067 Published by MDPI AG, Basel, Switzerland RSS E-Mail Table of Contents Alert