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Construction of citrus gene coexpression networks from microarray data using random matrix theory.

Du D, Rawat N, Deng Z, Gmitter FG - Hortic Res (2015)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Citrus Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida , Lake Alfred, FL 33850, USA.

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.

No MeSH data available.


Related in: MedlinePlus

Genes and edges in flesh-module 19.
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fig5: Genes and edges in flesh-module 19.

Mentions: Flesh-module 19 was also selected based on functional enrichment analyses. It has 11 nodes, 11 edges, and a density of 0.2 (Figure 5). The highest ranked KEGG pathway of this module was the citrate cycle (TCA cycle) (ath00020, p = 0.00026). The citrate cycle is the major pathway for the synthesis of citric acid, the most abundant organic acid in citrus46. At least three nodes of this module were related to the citrate cycle: Ciclev10008189m (dihydrolipoamide succinyltransferase gene), Ciclev10025308m (dihydrolipoamide acetyltransferase gene), and Ciclev10013692m (acyl-activating enzyme 5 gene). Two nodes were involved in the biosynthesis of the polyphenol compounds: Ciclev10019346m (UDP-glycosyltransferase gene) and Ciclev10011175m (phenylalanine ammonia lyase gene). One node, Ciclev10028195m (glucose-1-phosphate adenylyltransferase gene) was involved in glycogen biosynthesis. All these nodes were linked by Ciclev10006509m, which encodes a subunit of a RUB (Related to Ubiquitin)-activating enzyme. The proteins encoded by these genes may be subject to similar post-translational modifications.


Construction of citrus gene coexpression networks from microarray data using random matrix theory.

Du D, Rawat N, Deng Z, Gmitter FG - Hortic Res (2015)

Genes and edges in flesh-module 19.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4595991&req=5

fig5: Genes and edges in flesh-module 19.
Mentions: Flesh-module 19 was also selected based on functional enrichment analyses. It has 11 nodes, 11 edges, and a density of 0.2 (Figure 5). The highest ranked KEGG pathway of this module was the citrate cycle (TCA cycle) (ath00020, p = 0.00026). The citrate cycle is the major pathway for the synthesis of citric acid, the most abundant organic acid in citrus46. At least three nodes of this module were related to the citrate cycle: Ciclev10008189m (dihydrolipoamide succinyltransferase gene), Ciclev10025308m (dihydrolipoamide acetyltransferase gene), and Ciclev10013692m (acyl-activating enzyme 5 gene). Two nodes were involved in the biosynthesis of the polyphenol compounds: Ciclev10019346m (UDP-glycosyltransferase gene) and Ciclev10011175m (phenylalanine ammonia lyase gene). One node, Ciclev10028195m (glucose-1-phosphate adenylyltransferase gene) was involved in glycogen biosynthesis. All these nodes were linked by Ciclev10006509m, which encodes a subunit of a RUB (Related to Ubiquitin)-activating enzyme. The proteins encoded by these genes may be subject to similar post-translational modifications.

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Citrus Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida , Lake Alfred, FL 33850, USA.

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.

No MeSH data available.


Related in: MedlinePlus