ccNET: Database of co-expression networks with functional modules for diploid and polyploid Gossypium.
ccNET: Database of co-expression networks with functional modules for diploid and polyploid Gossypium.
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DOI：
10.1093/nar/gkw1342
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发表时间：
2017-05-19
影响因子：
14.9
通讯作者：
Su Z
中科院分区：
文献类型：
--
作者：
You Q;Xu W;Zhang K;Zhang L;Yi X;Yao D;Wang C;Zhang X;Zhao X;Provart NJ;Li F;Su Z
具有二倍体和多倍体物种的植物属是常见的进化现象。多倍体，特别是棉花和小麦等异源多倍体，是杂种优势研究的重要模型系统。在这里，我们整合了棉种的基因组序列和转录组数据，构建了共表达网络，并鉴定了来自不同棉种的功能模块，包括G中的1155和1884模块。 arboreumandG.分别为陆地草。我们将基因表达结果叠加到共表达网络上。我们进一步提供了二倍体和异源四倍体棉的直系同源基因的网络比较分析。我们还构建了 miRNA 目标网络并预测了这两种棉花的 PPI 网络。此外，我们将内部组蛋白修饰（H3K4me3）的 ChIP-seq 数据与顺式元件分析和基因集富集分析工具结合起来，用于研究棉属物种可能的基因调控机制。最后，我们构建了一个在线ccNET数据库（http://structuralbiology.cau.edu.cn/gossypium），用于二倍体和多倍体Gossypium物种的多维网络和表观基因组水平上的比较基因功能分析。 ccNET 数据库将有利于社区对棉花发育和胁迫响应过程中的基因/模块功能产生新的见解，并且可能有助于研究其他多倍体植物（例如棉花）的保护和多样性。小麦和甘蓝型油菜。
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 ofGossypiumspecies to construct co-expression networks and identified functional modules from different cotton species, including 1155 and 1884 modules inG. arboreumandG. 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 allotetraploidGossypium. 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 inGossypiumspecies. 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 polyploidGossypiumspecies. 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 asT. aestivumandBrassica napus.