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Article|10 Jun 2015|OPEN
Construction of citrus gene coexpression networks from microarray data using random matrix theory
Dongliang Du1 , Nidhi Rawat2 , Zhanao Deng2 and Fred G. Gmitter Jr.,1 ,
1Citrus Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, FL 33850, USA
2Gulf Coast Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, Wimauma, FL 33598, USA
*Corresponding author. E-mail: fgmitter@ufl.edu

Horticulture Research 2,
Article number: 26 (2015)
doi: https://doi.org/10.1038/hortres.2015.26
Views: 725

Received: 30 Mar 2015
Revised: 29 Apr 2015
Accepted: 04 May 2015
Published online: 10 Jun 2015

Abstract

After the sequencing of citrus genomes, gene function annotation is becoming a new challenge. Gene coexpression analysis can be employed for function annotation using publicly available microarray data sets. In this study, 230 sweet orange (Citrus sinensis) microarrays were used to construct seven coexpression networks, including one condition-independent and six condition-dependent (Citrus canker, Huanglongbing, leaves, flavedo, albedo, and flesh) networks. In total, these networks contain 37 633 edges among 6256 nodes (genes), which accounts for 52.11% measurable genes of the citrus microarray. Then, these networks were partitioned into functional modules using the Markov Cluster Algorithm. Significantly enriched Gene Ontology biological process terms and KEGG pathway terms were detected for 343 and 60 modules, respectively. Finally, independent verification of these networks was performed using another expression data of 371 genes. This study provides new targets for further functional analyses in citrus.