Bioinformatics
Abstract
Using large-scale RNA-seq samples, we constructed high coverage and confident GCNs in two monocot species rice and maize, and two eudicot species Arabidopsis and soybean, and subdivided them into co-expressed gene modules. Taking rice as an example, we discovered many interesting and valuable modules, for instance, pollen-specific modules and starch biosynthesis module. We explored the regulatory mechanism of modules and revealed synergistic effects of gene expression regulation. In addition, we discovered that the modules conserved among plants participated in basic biological processes, whereas the species-specific modules were involved in spatiotemporal-specific processes linking genotypes to phenotypes. Our study suggests gene regulatory relationships and modules relating to cellular activities and agronomic traits in several model and crop plants, and thus providing a valuable data source for plant genetics research and breeding.
| 论文编号: | DOI:10.1093/bioinformatics/bty642 |
| 论文题目: | Systematic Discovery of Novel and Valuable Plant Gene Modules by Large-scale RNA-seq Samples |
| 英文论文题目: | Systematic Discovery of Novel and Valuable Plant Gene Modules by Large-scale RNA-seq Samples |
| 第一作者: | Hua Yu, Lu Lu, Bingke Jiao, Chengzhi Liang |
| 英文第一作者: | Hua Yu, Lu Lu, Bingke Jiao, Chengzhi Liang |
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| 发表年度: | 2018-07-26 |
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| 摘要: | Using large-scale RNA-seq samples, we constructed high coverage and confident GCNs in two monocot species rice and maize, and two eudicot species Arabidopsis and soybean, and subdivided them into co-expressed gene modules. Taking rice as an example, we discovered many interesting and valuable modules, for instance, pollen-specific modules and starch biosynthesis module. We explored the regulatory mechanism of modules and revealed synergistic effects of gene expression regulation. In addition, we discovered that the modules conserved among plants participated in basic biological processes, whereas the species-specific modules were involved in spatiotemporal-specific processes linking genotypes to phenotypes. Our study suggests gene regulatory relationships and modules relating to cellular activities and agronomic traits in several model and crop plants, and thus providing a valuable data source for plant genetics research and breeding. |
| 英文摘要: | Using large-scale RNA-seq samples, we constructed high coverage and confident GCNs in two monocot species rice and maize, and two eudicot species Arabidopsis and soybean, and subdivided them into co-expressed gene modules. Taking rice as an example, we discovered many interesting and valuable modules, for instance, pollen-specific modules and starch biosynthesis module. We explored the regulatory mechanism of modules and revealed synergistic effects of gene expression regulation. In addition, we discovered that the modules conserved among plants participated in basic biological processes, whereas the species-specific modules were involved in spatiotemporal-specific processes linking genotypes to phenotypes. Our study suggests gene regulatory relationships and modules relating to cellular activities and agronomic traits in several model and crop plants, and thus providing a valuable data source for plant genetics research and breeding. |
| 刊物名称: | Bioinformatics |
| 英文刊物名称: | Bioinformatics |
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| 其它备注: | Hua Yu, Lu Lu, Bingke Jiao, Chengzhi Liang. Systematic discovery of novel and valuable plant gene modules by large-scale RNA-seq samples. Bioinformatics. DOI:10.1093/bioinformatics/bty642 |
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