alexa Construction of citrus gene coexpression networks from microarray data using random matrix theory.
Agri and Aquaculture

Agri and Aquaculture

Rice Research: Open Access

Author(s): Du D, Rawat N, Deng Z, Gmitter FG Jr, Du D, Rawat N, Deng Z, Gmitter FG Jr

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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.
This article was published in Hortic Res and referenced in Rice Research: Open Access

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