WheatCENet: A Database for Comparative Co-expression Networks Analysis of Allohexaploid Wheat and Its Progenitors.
WheatCENet: A Database for Comparative Co-expression Networks Analysis of Allohexaploid Wheat and Its Progenitors.
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WheatCENet：异源六倍体小麦及其祖先的比较共表达网络分析数据库
DOI：
10.1016/j.gpb.2022.04.007
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发表时间：
2023-04
影响因子：
9.5
通讯作者：
Su, Zhen
中科院分区：
文献类型：
--
作者：
Li, Zhongqiu;Hu, Yiheng;Ma, Xuelian;Da, Lingling;She, Jiajie;Liu, Yue;Yi, Xin;Cao, Yaxin;Xu, Wenying;Jiao, Yuannian;Su, Zhen
多倍体事件后的遗传和表观遗传变化可能导致基因表达的变化和调控网络的改变。本研究利用大规模转录组数据，构建了二倍体、四倍体和六倍体小麦的共表达网络，并建立了一个用于比较异源六倍体小麦及其祖先共表达网络的平台WheatCENet。WheatCENet是一个搜索和比较特定功能共表达网络，以及识别其中聚集的基因的相关功能的平台。功能注释，如通路，基因家族，蛋白-蛋白相互作用，microRNAs (miRNAs)，和几行表观基因组数据集成到这个平台，基因本体（GO）注释，基因集富集分析（GSEA），基序鉴定，和其他有用的工具也包括在内。利用WheatCENet，我们发现小麦异常穗组织1 （WAPO1）网络中与六倍体小麦穗发育相关的共表达基因比其祖先多。我们还在WAPO-A1的启动子区域发现了一个新的CCWWWWWWGG基序（CArG），这表明WAPO-A1基因的新功能化影响了六倍体小麦的小穗发育。WheatCENet可用于研究共表达网络和进行其他分析，从而促进小麦的比较和功能基因组研究。WheatCENet可在http://bioinformatics.cpolar.cn/WheatCENet和http://bioinformatics.cau.edu.cn/WheatCENet免费获得。
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 pathways, gene families, protein–protein interactions, microRNAs (miRNAs), 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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影响因子：
12.3
作者：
Alaux M;Rogers J;Letellier T;Flores R;Alfama F;Pommier C;Mohellibi N;Durand S;Kimmel E;Michotey C;Guerche C;Loaec M;Lainé M;Steinbach D;Choulet F;Rimbert H;Leroy P;Guilhot N;Salse J;Feuillet C;International Wheat Genome Sequencing Consortium;Paux E;Eversole K;Adam-Blondon AF;Quesneville H
通讯作者：
Quesneville H
影响因子：
11.4
作者：
Zhang B;Liu X;Zhao G;Mao X;Li A;Jing R
通讯作者：
Jing R
OsMADS57 和 OsTB1 之间的相互作用通过 DWARF14 调节水稻分蘖
影响因子：
16.6
作者：
通讯作者：
--
DOI：
10.1007/s00122-021-03781-7
发表时间：
2021-05
期刊：
TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik
影响因子：
--
作者：
Corsi B;Obinu L;Zanella CM;Cutrupi S;Day R;Geyer M;Lillemo M;Lin M;Mazza L;Percival-Alwyn L;Stadlmeier M;Mohler V;Hartl L;Cockram J
通讯作者：
Cockram J
影响因子：
56.9
作者：
Avni, Raz;Nave, Moran;Distelfeld, Assaf
通讯作者：
Distelfeld, Assaf