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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

Layout of the citrus “all data” coexpression network. The most overrepresented GO terms were shown for the 12 largest color-coded modules.
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fig2: Layout of the citrus “all data” coexpression network. The most overrepresented GO terms were shown for the 12 largest color-coded modules.

Mentions: Figure 2 displays the coexpression network of “all data” using Cytoscape 2.8.329. Although these networks have different numbers of nodes and edges, they have similar topological characteristics (Table 2). All these networks are composed of a major component and other small components. All nodes within one component are directly or indirectly connected. Nodes in the major components account for 62.56% to 82.28% of that in corresponding networks. The average path length of these networks ranges from 6.66 to 10.75, implying the small-world properties. The nodes degree of these networks fits to a power law distribution with the degree exponent (r) ranging from 1.13 to 2.10, indicating that these networks are scale free. These networks demonstrate modular and hierarchical characteristics with the average clustering coefficient ranging from 0.20 to 0.40, which is more than 36 times higher than that of same size random networks (data not shown). Table S2 provides a list of all edges in these networks. Taken together, these seven networks contain 37 633 edges among 6256 nodes (genes, Table S3), which account for 52.11% measurable genes of the microarray or 25.50% total genes in C. x clementina v1.0 genome. Table 3 shows the intersections between nodes and edges of these networks. Generally, the intersections among them are relatively low. In total, 3304 nodes (52.81%) and 34 860 edges (92.63%) were found only in one network. The intersection among “leaves”, “all data”, and “citrus canker” network is relatively higher than that between other networks.


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

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

Layout of the citrus “all data” coexpression network. The most overrepresented GO terms were shown for the 12 largest color-coded modules.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

fig2: Layout of the citrus “all data” coexpression network. The most overrepresented GO terms were shown for the 12 largest color-coded modules.
Mentions: Figure 2 displays the coexpression network of “all data” using Cytoscape 2.8.329. Although these networks have different numbers of nodes and edges, they have similar topological characteristics (Table 2). All these networks are composed of a major component and other small components. All nodes within one component are directly or indirectly connected. Nodes in the major components account for 62.56% to 82.28% of that in corresponding networks. The average path length of these networks ranges from 6.66 to 10.75, implying the small-world properties. The nodes degree of these networks fits to a power law distribution with the degree exponent (r) ranging from 1.13 to 2.10, indicating that these networks are scale free. These networks demonstrate modular and hierarchical characteristics with the average clustering coefficient ranging from 0.20 to 0.40, which is more than 36 times higher than that of same size random networks (data not shown). Table S2 provides a list of all edges in these networks. Taken together, these seven networks contain 37 633 edges among 6256 nodes (genes, Table S3), which account for 52.11% measurable genes of the microarray or 25.50% total genes in C. x clementina v1.0 genome. Table 3 shows the intersections between nodes and edges of these networks. Generally, the intersections among them are relatively low. In total, 3304 nodes (52.81%) and 34 860 edges (92.63%) were found only in one network. The intersection among “leaves”, “all data”, and “citrus canker” network is relatively higher than that between other networks.

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