Limits...
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

Graph showing coexpressed genes of the C. clementina homolog of citrus LOB1 (Ciclev10033956m) and SWEET1 (Ciclev10002276m) in canker-module 1.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4595991&req=5

fig3: Graph showing coexpressed genes of the C. clementina homolog of citrus LOB1 (Ciclev10033956m) and SWEET1 (Ciclev10002276m) in canker-module 1.

Mentions: The guide-gene approach is commonly used to explore functional modules from gene coexpression networks. A lateral organ boundaries 1 (CsLOB1) gene has recently been identified as a citrus canker disease susceptibility gene in sweet orange42. The precise function of CsLOB1 is still not clear. Using its homolog in C. x clementina (Ciclev10033956m) as a guide, 25 coexpressed genes were identified in module 1 of the “citrus canker” network (Figure 3). Six of them were involved in cell wall metabolism: Ciclev10005888m (plant pectin methylesterase inhibitor superfamily protein), Ciclev10016123m (xyloglucan endotransglucosylase/hydrolase 5), Ciclev10021623m (expansin B2), Ciclev10007670m (proline-rich extensin-like receptor kinase), Ciclev10014994m (glycosyl hydrolase), and Ciclev10019941m (pectin lyase-like superfamily protein). Similar results were reported in the NICCE networks17. Interestingly, three minichromosome maintenance family genes (Ciclev10007588m, Ciclev10027769m, and Ciclev10019324m) were coexpressed with Ciclev10033956m, implying the functions of LOB1 in DNA replication. Another candidate target of TAL effectors, CsSWEET1 (Ciclev10002276m)42, was also included in module 1 of the “citrus canker” network. It encodes a sugar transporter for pathogen nutrition and is linked to Ciclev10033956m through three nodes (the shortest path).


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

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

Graph showing coexpressed genes of the C. clementina homolog of citrus LOB1 (Ciclev10033956m) and SWEET1 (Ciclev10002276m) in canker-module 1.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

fig3: Graph showing coexpressed genes of the C. clementina homolog of citrus LOB1 (Ciclev10033956m) and SWEET1 (Ciclev10002276m) in canker-module 1.
Mentions: The guide-gene approach is commonly used to explore functional modules from gene coexpression networks. A lateral organ boundaries 1 (CsLOB1) gene has recently been identified as a citrus canker disease susceptibility gene in sweet orange42. The precise function of CsLOB1 is still not clear. Using its homolog in C. x clementina (Ciclev10033956m) as a guide, 25 coexpressed genes were identified in module 1 of the “citrus canker” network (Figure 3). Six of them were involved in cell wall metabolism: Ciclev10005888m (plant pectin methylesterase inhibitor superfamily protein), Ciclev10016123m (xyloglucan endotransglucosylase/hydrolase 5), Ciclev10021623m (expansin B2), Ciclev10007670m (proline-rich extensin-like receptor kinase), Ciclev10014994m (glycosyl hydrolase), and Ciclev10019941m (pectin lyase-like superfamily protein). Similar results were reported in the NICCE networks17. Interestingly, three minichromosome maintenance family genes (Ciclev10007588m, Ciclev10027769m, and Ciclev10019324m) were coexpressed with Ciclev10033956m, implying the functions of LOB1 in DNA replication. Another candidate target of TAL effectors, CsSWEET1 (Ciclev10002276m)42, was also included in module 1 of the “citrus canker” network. It encodes a sugar transporter for pathogen nutrition and is linked to Ciclev10033956m through three nodes (the shortest path).

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