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Nucleic Acids Res. 2017 Jan 4;45(D1):D1090-D1099. doi: 10.1093/nar/gkw910. Epub 2016 Oct 7.

ccNET: Database of co-expression networks with functional modules for diploid and polyploid Gossypium.

Author information

1
State key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China.
2
State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agriculture Sciences (CAAS), Anyang, Henan 455000, China.
3
Department of Cell & Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, 25 Willcocks St, Toronto, ON M5S 3B2, Canada.
4
State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agriculture Sciences (CAAS), Anyang, Henan 455000, China aylifug@163.com.
5
State key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China zhensu@cau.edu.cn.

Abstract

Plant genera with both diploid and polyploid species are a common evolutionary occurrence. Polyploids, especially allopolyploids such as cotton and wheat, are a great model system for heterosis research. Here, we have integrated genome sequences and transcriptome data of Gossypium species to construct co-expression networks and identified functional modules from different cotton species, including 1155 and 1884 modules in G. arboreum and G. hirsutum, respectively. We overlayed the gene expression results onto the co-expression network. We further provided network comparison analysis for orthologous genes across the diploid and allotetraploid Gossypium We also constructed miRNA-target networks and predicted PPI networks for both cotton species. Furthermore, we integrated in-house ChIP-seq data of histone modification (H3K4me3) together with cis-element analysis and gene sets enrichment analysis tools for studying possible gene regulatory mechanism in Gossypium species. Finally, we have constructed an online ccNET database (http://structuralbiology.cau.edu.cn/gossypium) for comparative gene functional analyses at a multi-dimensional network and epigenomic level across diploid and polyploid Gossypium species. The ccNET database will be beneficial for community to yield novel insights into gene/module functions during cotton development and stress response, and might be useful for studying conservation and diversity in other polyploid plants, such as T. aestivum and Brassica napus.

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