• 文献检索
  • 文档翻译
  • 深度研究
  • 学术资讯
  • Suppr Zotero 插件Zotero 插件
  • 邀请有礼
  • 套餐&价格
  • 历史记录
应用&插件
Suppr Zotero 插件Zotero 插件浏览器插件Mac 客户端Windows 客户端微信小程序
定价
高级版会员购买积分包购买API积分包
服务
文献检索文档翻译深度研究API 文档MCP 服务
关于我们
关于 Suppr公司介绍联系我们用户协议隐私条款
关注我们

Suppr 超能文献

核心技术专利：CN118964589B侵权必究
粤ICP备2023148730 号-1Suppr @ 2026

文献检索

告别复杂PubMed语法，用中文像聊天一样搜索，搜遍4000万医学文献。AI智能推荐，让科研检索更轻松。

立即免费搜索

文件翻译

保留排版，准确专业，支持PDF/Word/PPT等文件格式，支持 12+语言互译。

免费翻译文档

深度研究

AI帮你快速写综述，25分钟生成高质量综述，智能提取关键信息，辅助科研写作。

立即免费体验

使用综合图谱数据库研究转录调控。

GREG-studying transcriptional regulation using integrative graph databases.

机构信息

School of Basic Medical Sciences, Guangzhou Medical University, Panyu Campus of Guangzhou Medical University, Xinzao, 511436 Guangzhou, P.R. China.

Joint School of Life Sciences, Guangzhou Medical University and Guangzhou Institutes of Biomedicine and Health (Chinese Academy of Sciences), Panyu Campus of Guangzhou Medical University, Xinzao, 511436 Guangzhou, P.R. China.

出版信息

Database (Oxford). 2020 Jan 1;2020. doi: 10.1093/database/baz162.

DOI:10.1093/database/baz162
PMID:32055858
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC7018612/
Abstract

A gene regulatory process is the result of the concerted action of transcription factors, co-factors, regulatory non-coding RNAs (ncRNAs) and chromatin interactions. Therefore, the combination of protein-DNA, protein-protein, ncRNA-DNA, ncRNA-protein and DNA-DNA data in a single graph database offers new possibilities regarding generation of biological hypotheses. GREG (The Gene Regulation Graph Database) is an integrative database and web resource that allows the user to visualize and explore the network of all above-mentioned interactions for a query transcription factor, long non-coding RNA, genomic range or DNA annotation, as well as extracting node and interaction information, identifying connected nodes and performing advanced graphical queries directly on the regulatory network, in a simple and efficient way. In this article, we introduce GREG together with some application examples (including exploratory research of Nanog's regulatory landscape and the etiology of chronic obstructive pulmonary disease), which we use as a demonstration of the advantages of using graph databases in biomedical research. Database URL: https://mora-lab.github.io/projects/greg.html, www.moralab.science/GREG/.

摘要

基因调控过程是转录因子、共因子、调控非编码 RNA（ncRNA）和染色质相互作用协同作用的结果。因此，将蛋白质-DNA、蛋白质-蛋白质、ncRNA-DNA、ncRNA-蛋白质和 DNA-DNA 数据组合在单个图形数据库中，为生成生物学假设提供了新的可能性。GREG（基因调控图形数据库）是一个集成的数据库和网络资源，允许用户可视化和探索查询转录因子、长非编码 RNA、基因组范围或 DNA 注释的所有上述相互作用的网络，以及提取节点和交互信息，识别连接节点，并以简单有效的方式直接在调控网络上执行高级图形查询。在本文中，我们介绍了 GREG 及其一些应用示例（包括对 Nanog 调控景观和慢性阻塞性肺疾病病因的探索性研究），我们将其用作在生物医学研究中使用图形数据库的优势的演示。数据库网址：https://mora-lab.github.io/projects/greg.html，www.moralab.science/GREG/。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c995/7018612/6e5a0773ca59/baz162f2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c995/7018612/387e7eaa2018/baz162f1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c995/7018612/6e5a0773ca59/baz162f2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c995/7018612/387e7eaa2018/baz162f1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c995/7018612/6e5a0773ca59/baz162f2.jpg

相似文献

1
GREG-studying transcriptional regulation using integrative graph databases.使用综合图谱数据库研究转录调控。
Database (Oxford). 2020 Jan 1;2020. doi: 10.1093/database/baz162.
2
CoryneRegNet: an ontology-based data warehouse of corynebacterial transcription factors and regulatory networks.棒状杆菌调控网络数据库（CoryneRegNet）：一个基于本体的棒状杆菌转录因子和调控网络数据仓库。
BMC Genomics. 2006 Feb 14;7:24. doi: 10.1186/1471-2164-7-24.
3
Update of the FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation.FANTOM网络资源更新：从哺乳动物转录图谱到其动态调控
Nucleic Acids Res. 2011 Jan;39(Database issue):D856-60. doi: 10.1093/nar/gkq1112. Epub 2010 Nov 12.
4
A new advance in alternative splicing databases: from catalogue to detailed analysis of regulation of expression and function of human alternative splicing variants.可变剪接数据库的一项新进展：从目录到对人类可变剪接变体表达和功能调控的详细分析。
BMC Bioinformatics. 2007 Jun 4;8:180. doi: 10.1186/1471-2105-8-180.
5
EnhancerDB: a resource of transcriptional regulation in the context of enhancers.EnhancerDB：增强子调控转录的资源数据库。
Database (Oxford). 2019 Jan 1;2019:bay141. doi: 10.1093/database/bay141.
6
Co-LncRNA: investigating the lncRNA combinatorial effects in GO annotations and KEGG pathways based on human RNA-Seq data.共长链非编码RNA：基于人类RNA测序数据研究长链非编码RNA在基因本体注释和京都基因与基因组百科全书通路中的组合效应。
Database (Oxford). 2015 Sep 10;2015. doi: 10.1093/database/bav082. Print 2015.
7
RegNetwork: an integrated database of transcriptional and post-transcriptional regulatory networks in human and mouse.RegNetwork：人类和小鼠转录及转录后调控网络的综合数据库。
Database (Oxford). 2015 Sep 30;2015. doi: 10.1093/database/bav095. Print 2015.
8
HRGRN: A Graph Search-Empowered Integrative Database of Arabidopsis Signaling Transduction, Metabolism and Gene Regulation Networks.HRGRN：一个由图形搜索支持的拟南芥信号转导、代谢和基因调控网络综合数据库。
Plant Cell Physiol. 2016 Jan;57(1):e12. doi: 10.1093/pcp/pcv200. Epub 2015 Dec 12.
9
RAIN: RNA-protein Association and Interaction Networks.RAIN：RNA-蛋白质关联与相互作用网络
Database (Oxford). 2017 Jan 10;2017. doi: 10.1093/database/baw167. Print 2017.
10
ORegAnno: an open access database and curation system for literature-derived promoters, transcription factor binding sites and regulatory variation.ORegAnno：一个用于文献衍生启动子、转录因子结合位点和调控变异的开放获取数据库及注释系统。
Bioinformatics. 2006 Mar 1;22(5):637-40. doi: 10.1093/bioinformatics/btk027. Epub 2006 Jan 5.

引用本文的文献

1
Graph databases in systems biology: a systematic review.系统生物学中的图数据库：系统评价。
Brief Bioinform. 2024 Sep 23;25(6). doi: 10.1093/bib/bbae561.
2
Chromatin Hubs: A biological and computational outlook.染色质枢纽：生物学与计算视角
Comput Struct Biotechnol J. 2022 Jul 5;20:3796-3813. doi: 10.1016/j.csbj.2022.07.002. eCollection 2022.
3
FGDB: a comprehensive graph database of ligand fragments from the Protein Data Bank.FGDB：蛋白质数据库中配体片段的综合图数据库。

本文引用的文献

1
Involvement of Lamin B1 Reduction in Accelerated Cellular Senescence during Chronic Obstructive Pulmonary Disease Pathogenesis.层粘连蛋白 B1 减少参与慢性阻塞性肺疾病发病过程中的细胞加速衰老。
J Immunol. 2019 Mar 1;202(5):1428-1440. doi: 10.4049/jimmunol.1801293. Epub 2019 Jan 28.
2
Cistrome Data Browser: expanded datasets and new tools for gene regulatory analysis.染色质数据浏览器：扩展数据集和新的基因调控分析工具。
Nucleic Acids Res. 2019 Jan 8;47(D1):D729-D735. doi: 10.1093/nar/gky1094.
3
BioGraph: a web application and a graph database for querying and analyzing bioinformatics resources.
Database (Oxford). 2022 Jun 27;2022. doi: 10.1093/database/baac044.
4
An overview of graph databases and their applications in the biomedical domain.图数据库及其在生物医学领域中的应用概述。
Database (Oxford). 2021 May 18;2021. doi: 10.1093/database/baab026.
BioGraph：一个用于查询和分析生物信息学资源的网络应用程序和图形数据库。
BMC Syst Biol. 2018 Nov 20;12(Suppl 5):98. doi: 10.1186/s12918-018-0616-4.
4
GENCODE reference annotation for the human and mouse genomes.GENCODE 人类和小鼠基因组参考注释。
Nucleic Acids Res. 2019 Jan 8;47(D1):D766-D773. doi: 10.1093/nar/gky955.
5
LnChrom: a resource of experimentally validated lncRNA-chromatin interactions in human and mouse.LnChrom：人类和小鼠中经过实验验证的 lncRNA-染色质相互作用的资源。
Database (Oxford). 2018 Jan 1;2018. doi: 10.1093/database/bay039.
6
Reactome graph database: Efficient access to complex pathway data.Reactome 图形数据库：高效访问复杂的通路数据。
PLoS Comput Biol. 2018 Jan 29;14(1):e1005968. doi: 10.1371/journal.pcbi.1005968. eCollection 2018 Jan.
7
MELODI: Mining Enriched Literature Objects to Derive Intermediates.MELODI：挖掘丰富的文献对象以推导中间体。
Int J Epidemiol. 2018 Jan 12;47(2):369-79. doi: 10.1093/ije/dyx251.
8
Super-Enhancers at the Nanog Locus Differentially Regulate Neighboring Pluripotency-Associated Genes.Nanog基因座处的超级增强子差异调节相邻的多能性相关基因。
Cell Rep. 2016 Sep 27;17(1):19-28. doi: 10.1016/j.celrep.2016.09.002.
9
Candidate genes for COPD: current evidence and research.慢性阻塞性肺疾病的候选基因：当前证据与研究
Int J Chron Obstruct Pulmon Dis. 2015 Oct 19;10:2249-55. doi: 10.2147/COPD.S80227. eCollection 2015.
10
cyNeo4j: connecting Neo4j and Cytoscape.cyNeo4j：连接Neo4j和Cytoscape。
Bioinformatics. 2015 Dec 1;31(23):3868-9. doi: 10.1093/bioinformatics/btv460. Epub 2015 Aug 12.