生物
基因
转录组
计算生物学
遗传学
表观遗传学
基因本体论
基因调控网络
基因注释
基因表达谱
基因表达
基因组
作者
Zhongqiu Li,Yiheng Hu,Xuelian Ma,Da Lingling,Jiajie She,Yue Liu,Xin Yi,Yuhua Wang,Wenying Xu,Yuannian Jiao,Zhen Su
标识
DOI:10.1016/j.gpb.2022.04.007
摘要
Genetic and epigenetic changes after polyploidization events could result in variable gene expression and modified regulatory networks. Here, using large-scale transcriptome data, we constructed co-expression networks for diploid, tetraploid, and hexaploid wheat species, and built a platform for comparing co-expression networks of allohexaploid wheat and its progenitors, named WheatCENet. WheatCENet is a platform for searching and comparing specific functional co-expression networks, as well as identifying the related functions of the genes clustered therein. Functional annotations like pathway, gene family, protein-protein interactions, microRNA (miRNA), and several lines of epigenome data are integrated into this platform, and gene ontology (GO) annotation, gene set enrichment analysis (GSEA), motif identification, and other useful tools are also included. Using WheatCENet, we found that the network of WHEAT ABERRANT PANICLE ORGANIZATION 1 ( WAPO1 ) has more co-expressed genes related to spike development in hexaploid wheat than its progenitors. We also found a novel motif of CCWWWWWWGG (CArG) specifically in the promoter region of WAPO-A1 , suggesting that neofunctionalization of the WAPO-A1 gene affects spikelet development in hexaploid wheat. WheatCENet is useful for investigating co-expression networks and conducting other analyses, and thus facilitates comparative and functional genomic studies in wheat. WheatCENet is freely available at http://bioinformatics.cpolar.cn/ WheatCENet and http://bioinformatics.cau.edu.cn/WheatCENet.
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