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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 HLB-module 6.
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fig6: Genes and edges in HLB-module 6.

Mentions: HLB-module 6 has 28 nodes, 75 edges, and a density of 0.198 (Figure 6). This module was selected because 13 of these 28 genes (46.43%) were only included in “HLB” network. Seventeen genes were assigned to specific GO terms. The highest ranked GO term of this module was programmed cell death (PCD, GO: 0012501, p = 0.005). PCD is widely observed in plants in response to pathogenic infection. At least eight genes in this module were related to PCD. Bcl-2-associated athanogene gene (Ciclev10018596m) plays a critical role in PCD47. It can suppress PCD via its interaction with Hsc70 and Hsp40 (Ciclev10000372m)48. However, the up-regulation of genes involved in the ubiquitin-proteasome system can activate PCD49. Ciclev10008240m (polyubiquitin 10) and Ciclev10005221m (RING finger E3 ubiquitin ligases) are parts of the ubiquitin-proteasome system. Other genes related to PCD include: Ciclev10005800m (myosin heavy chain-related), Ciclev10032432m (sphingoid base hydroxylase), Ciclev10021281m (LAG1 longevity assurance homolog 3), and Ciclev10032631m (Glutaredoxin family protein). Their functions in HLB still need to be determined.


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 HLB-module 6.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

fig6: Genes and edges in HLB-module 6.
Mentions: HLB-module 6 has 28 nodes, 75 edges, and a density of 0.198 (Figure 6). This module was selected because 13 of these 28 genes (46.43%) were only included in “HLB” network. Seventeen genes were assigned to specific GO terms. The highest ranked GO term of this module was programmed cell death (PCD, GO: 0012501, p = 0.005). PCD is widely observed in plants in response to pathogenic infection. At least eight genes in this module were related to PCD. Bcl-2-associated athanogene gene (Ciclev10018596m) plays a critical role in PCD47. It can suppress PCD via its interaction with Hsc70 and Hsp40 (Ciclev10000372m)48. However, the up-regulation of genes involved in the ubiquitin-proteasome system can activate PCD49. Ciclev10008240m (polyubiquitin 10) and Ciclev10005221m (RING finger E3 ubiquitin ligases) are parts of the ubiquitin-proteasome system. Other genes related to PCD include: Ciclev10005800m (myosin heavy chain-related), Ciclev10032432m (sphingoid base hydroxylase), Ciclev10021281m (LAG1 longevity assurance homolog 3), and Ciclev10032631m (Glutaredoxin family protein). Their functions in HLB still need to be determined.

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