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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 canker-module 25.
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fig4: Genes and edges in canker-module 25.

Mentions: Canker-module 25 was selected based on functional enrichment analyses. It has 10 nodes, 14 edges and a density of 0.311 (Figure 4). The highest ranked (lowest p value) GO term of this module was response to oxidative stress (GO: 0006979, p = 0.05). The highest ranked KEGG pathway of this module was plant hormone signal transduction (ath04075, p = 0.00024). Increased ethylene production was reported in citrus leaves inoculated with Xanthomonas campestris pv. citri (Hasse) Dye (Xc), a strain of bacteria that causes citrus canker43. However, the ethylene signal transduction pathway is not clear in citrus. Three nodes in this module, Ciclev10019132m (ERS1, ethylene response sensor 1), Ciclev10021170m (MAP kinase kinase) and Ciclev10005820m (ERF1, ethylene response factor 1), may be involved in the ethylene signal transduction. The hub gene of this module is Ciclev10019132m (ERS1). In Arabidopsis, ethylene signal is first perceived by endoplasmic reticulum localized receptor (including ERS1) and then transduced to ERF and downstream targets through MAPK cascades44,45. A jasmonic acid-amido synthetase gene (Ciclev10019459m) and a protein phosphatase 2C gene (Ciclev10004981m) were also included in this module, implying the cross-talk among ethylene, JA and ABA signaling pathways. Other genes may also be involved in plant hormone signal transduction, such as Ciclev10024032m (cysteine-rich receptor-like protein kinase) and Ciclev10001726m (peroxidase gene). Therefore, canker-module 25 is likely to carry on the functions of plant hormone signal transduction. Unannotated genes in this module would be hypothesized to be related to plant hormone signal transduction.


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 canker-module 25.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

fig4: Genes and edges in canker-module 25.
Mentions: Canker-module 25 was selected based on functional enrichment analyses. It has 10 nodes, 14 edges and a density of 0.311 (Figure 4). The highest ranked (lowest p value) GO term of this module was response to oxidative stress (GO: 0006979, p = 0.05). The highest ranked KEGG pathway of this module was plant hormone signal transduction (ath04075, p = 0.00024). Increased ethylene production was reported in citrus leaves inoculated with Xanthomonas campestris pv. citri (Hasse) Dye (Xc), a strain of bacteria that causes citrus canker43. However, the ethylene signal transduction pathway is not clear in citrus. Three nodes in this module, Ciclev10019132m (ERS1, ethylene response sensor 1), Ciclev10021170m (MAP kinase kinase) and Ciclev10005820m (ERF1, ethylene response factor 1), may be involved in the ethylene signal transduction. The hub gene of this module is Ciclev10019132m (ERS1). In Arabidopsis, ethylene signal is first perceived by endoplasmic reticulum localized receptor (including ERS1) and then transduced to ERF and downstream targets through MAPK cascades44,45. A jasmonic acid-amido synthetase gene (Ciclev10019459m) and a protein phosphatase 2C gene (Ciclev10004981m) were also included in this module, implying the cross-talk among ethylene, JA and ABA signaling pathways. Other genes may also be involved in plant hormone signal transduction, such as Ciclev10024032m (cysteine-rich receptor-like protein kinase) and Ciclev10001726m (peroxidase gene). Therefore, canker-module 25 is likely to carry on the functions of plant hormone signal transduction. Unannotated genes in this module would be hypothesized to be related to plant hormone signal transduction.

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