dbEmbryo multi-omics database for analyses of synergistic regulation in early mammalian embryo development.
dbEmbryo multi-omics database for analyses of synergistic regulation in early mammalian embryo development.
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dbEmbryo 多组学数据库，用于分析早期哺乳动物胚胎发育的协同调控
DOI：
10.1101/gr.276744.122
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发表时间：
2022-08-25
期刊：
影响因子：
7
通讯作者：
Chen, Hebing
中科院分区：
文献类型：
--
作者：
Huang, Xin;Tang, Xiaohan;Bai, Xuemei;Li, Honglei;Tao, Huan;Wang, Junting;Li, Yaru;Sun, Yu;Zheng, Yang;Xu, Xiang;Wang, Longteng;Ding, Yang;Lu, Meisong;Zhou, Pingkun;Bo, Xiaochen;Li, Hao;Chen, Hebing
在哺乳动物早期胚胎发育过程中，不同的表观遗传标记经历重编程，并在基因表达的介导中发挥关键作用。目前，几个数据库提供了早期胚胎的多组学信息。然而，相互关联的表观遗传标记如何共同发挥作用以时空方式协调遗传密码的表达仍然难以分析，这明显限制了科学和临床研究。在这里，我们介绍了dbEmbryo，一个用于人类和小鼠早期胚胎的集成和交互式多组学数据库。dbEmbryo整合了人类和小鼠早期胚胎的基因表达，DNA甲基化，组蛋白修饰，染色质可及性和高阶染色质结构谱的数据。它集成了定制的分析工具，如“多组学可视化”，“基因和峰值注释”，“ZGA基因簇”，“顺式调控”，“协同调控”，“启动子信号富集”和“3D基因组”。用户可以检索基因表达和表观遗传图谱模式，以分析不同早期胚胎发育阶段的协同变化。我们展示了dbEmbryo在包含早期胚胎发育数据的现有数据库中的独特性，并提供了概述。使用dbEmbryo，我们获得了早期胚胎发育过程中转录控制的阶段分离模型。dbEmbryo为生物学家和临床医生提供基于网络的分析工具和全面的资源，以破译人类和小鼠早期胚胎发育的分子调控机制。
During early mammalian embryo development, different epigenetic marks undergo reprogramming and play crucial roles in the mediation of gene expression. Currently, several databases provide multi-omics information on early embryos. However, how interconnected epigenetic markers function together to coordinate the expression of the genetic code in a spatiotemporal manner remains difficult to analyze, markedly limiting scientific and clinical research. Here, we present dbEmbryo, an integrated and interactive multi-omics database for human and mouse early embryos. dbEmbryo integrates data on gene expression, DNA methylation, histone modifications, chromatin accessibility, and higher-order chromatin structure profiles for human and mouse early embryos. It incorporates customized analysis tools, such as “multi-omics visualization,” “Gene&Peak annotation,” “ZGA gene cluster,” “cis-regulation,” “synergistic regulation,” “promoter signal enrichment,” and “3D genome.” Users can retrieve gene expression and epigenetic profile patterns to analyze synergistic changes across different early embryo developmental stages. We showed the uniqueness of dbEmbryo among extant databases containing data on early embryo development and provided an overview. Using dbEmbryo, we obtained a phase-separated model of transcriptional control during early embryo development. dbEmbryo offers web-based analytical tools and a comprehensive resource for biologists and clinicians to decipher molecular regulatory mechanisms of human and mouse early embryo development.
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DOI：
10.1093/bioinformatics/btr064
发表时间：
2011-04-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Grant CE;Bailey TL;Noble WS
通讯作者：
Noble WS
影响因子：
12.3
作者：
Buels R;Yao E;Diesh CM;Hayes RD;Munoz-Torres M;Helt G;Goodstein DM;Elsik CG;Lewis SE;Stein L;Holmes IH
通讯作者：
Holmes IH
影响因子：
64.5
作者：
Dowen JM;Fan ZP;Hnisz D;Ren G;Abraham BJ;Zhang LN;Weintraub AS;Schujiers J;Lee TI;Zhao K;Young RA
通讯作者：
Young RA
影响因子：
23.9
作者：
Ji X;Dadon DB;Powell BE;Fan ZP;Borges-Rivera D;Shachar S;Weintraub AS;Hnisz D;Pegoraro G;Lee TI;Misteli T;Jaenisch R;Young RA
通讯作者：
Young RA
影响因子：
64.5
作者：
Lu F;Liu Y;Inoue A;Suzuki T;Zhao K;Zhang Y
通讯作者：
Zhang Y