Curating the innate immunity interactome.
Curating the innate immunity interactome.
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DOI：
10.1186/1752-0509-4-117
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发表时间：
2010-08-20
影响因子：
--
通讯作者：
Hancock RE
中科院分区：
文献类型：
--
作者：
Lynn DJ;Chan C;Naseer M;Yau M;Lo R;Sribnaia A;Ring G;Que J;Wee K;Winsor GL;Laird MR;Breuer K;Foroushani AK;Brinkman FS;Hancock RE
先天免疫反应是抵抗入侵病原体的第一道防线，并受到复杂的信号传导和转录网络的调节。系统生物学方法有望通过对这些网络的分析和建模，为先天免疫的调节提供新的思路。在这个过程中的一个关键的初始步骤是上下文编目的组成部分，这个系统和分子相互作用，包括这些网络。InnateDB（www.innatedb.com）是一个分子相互作用和途径数据库，旨在促进先天免疫的系统水平分析。在这里，我们描述了InnateDB策展项目，该项目以丰富的上下文细节手动注释人类和小鼠先天免疫相互作用组，并介绍了我们的新型策展软件系统，该系统已开发用于确保以高度准确和符合数据标准的方式策展交互。到目前为止，已经从生物医学文献中收集了超过13，000种相互作用（蛋白质，DNA和RNA）。在这里，我们提供的数据，说明了先天免疫相互作用组的InnateDB策展如何极大地增强了可用于系统级分析的网络和途径注释，并讨论了这种策展工作面临的挑战。值得注意的是，我们提供了几条证据，先天免疫相互作用组的分析有可能确定新的信号，转录和转录后调节先天免疫。此外，这些分析还提供了对先天免疫途径与其他生物过程（如适应性免疫、癌症和糖尿病）之间的相互作用的深入了解，有趣的是，这些分析表明了与其他途径的联系，这些途径尚未涉及先天免疫反应。总之，对InnateDB相互作用组的管理提供了丰富的信息，以实现先天免疫的系统级分析。
The innate immune response is the first line of defence against invading pathogens and is regulated by complex signalling and transcriptional networks. Systems biology approaches promise to shed new light on the regulation of innate immunity through the analysis and modelling of these networks. A key initial step in this process is the contextual cataloguing of the components of this system and the molecular interactions that comprise these networks. InnateDB (http://www.innatedb.com) is a molecular interaction and pathway database developed to facilitate systems-level analyses of innate immunity. Here, we describe the InnateDB curation project, which is manually annotating the human and mouse innate immunity interactome in rich contextual detail, and present our novel curation software system, which has been developed to ensure interactions are curated in a highly accurate and data-standards compliant manner. To date, over 13,000 interactions (protein, DNA and RNA) have been curated from the biomedical literature. Here, we present data, illustrating how InnateDB curation of the innate immunity interactome has greatly enhanced network and pathway annotation available for systems-level analysis and discuss the challenges that face such curation efforts. Significantly, we provide several lines of evidence that analysis of the innate immunity interactome has the potential to identify novel signalling, transcriptional and post-transcriptional regulators of innate immunity. Additionally, these analyses also provide insight into the cross-talk between innate immunity pathways and other biological processes, such as adaptive immunity, cancer and diabetes, and intriguingly, suggests links to other pathways, which as yet, have not been implicated in the innate immune response. In summary, curation of the InnateDB interactome provides a wealth of information to enable systems-level analysis of innate immunity.
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影响因子：
14.9
作者：
Bruford, Elspeth A.;Lush, Michael J.;Wright, Mathew W.;Sneddon, Tam P.;Povey, Sue;Birney, Ewan
通讯作者：
Birney, Ewan
影响因子：
3
作者：
Kabiljo R;Clegg AB;Shepherd AJ
通讯作者：
Shepherd AJ
影响因子：
14.9
作者：
Chatr-aryamontri, Andrew;Ceol, Arnaud;Palazzi, Luisa Montecchi;Nardelli, Giuliano;Schneider, Maria Victoria;Castagnoli, Luisa;Cesareni, Gianni
通讯作者：
Cesareni, Gianni
影响因子：
3.7
作者：
Alexiou P;Maragkakis M;Papadopoulos GL;Simmosis VA;Zhang L;Hatzigeorgiou AG
通讯作者：
Hatzigeorgiou AG
DOI：
10.1126/science.1183021
发表时间：
2010-01-15
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Iwasaki A;Medzhitov R
通讯作者：
Medzhitov R