EcID. A database for the inference of functional interactions in E. coli.
EcID. A database for the inference of functional interactions in E. coli.
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DOI：
10.1093/nar/gkn853
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发表时间：
2009-01
影响因子：
14.9
通讯作者：
Juan D
中科院分区：
文献类型：
--
作者：
Andres Leon E;Ezkurdia I;García B;Valencia A;Juan D
ECID数据库(大肠杆菌相互作用数据库)提供了一个框架，用于整合从以下来源提取的关于功能相互作用的信息：EcoCyc(代谢途径、蛋白质复合体和调节信息)、KEGG(代谢途径)、MINT和INTERNAL(蛋白质相互作用)。它还包括来自两个大肠杆菌高通量下拉实验的蛋白质复合体的信息，以及使用与IHOP文本挖掘系统相关联的网络服务从文献中提取的潜在相互作用。此外，ECID结合了各种预测方法的结果，包括两种基于基因组信息的蛋白质相互作用预测方法(系统发育概况和基因邻域)和三种基于共同进化分析的方法(镜像树、在Silico 2杂交中和上下文镜像)。ECID将专门制定的置信度分数与每个预测相关联。ECID与其他系统不同的两个主要特征是基于共同进化的预测与实验数据的结合，以及大肠杆菌特异性信息的引入，如来自EcoCyc的基因调控信息。ECID数据库信息的组合提供的可能性通过对一组与yeaG相关的特征不佳的基因的潜在功能的预测来说明。ECID可在线获取，网址为http://ecid.bioinfo.cnio.es.
The EcID database (Escherichia coli Interaction Database) provides a framework for the integration of information on functional interactions extracted from the following sources: EcoCyc (metabolic pathways, protein complexes and regulatory information), KEGG (metabolic pathways), MINT and IntAct (protein interactions). It also includes information on protein complexes from the two E. coli high-throughput pull-down experiments and potential interactions extracted from the literature using the web services associated to the iHOP text-mining system. Additionally, EcID incorporates results of various prediction methods, including two protein interaction prediction methods based on genomic information (Phylogenetic Profiles and Gene Neighbourhoods) and three methods based on the analysis of co-evolution (Mirror Tree, In Silico 2 Hybrid and Context Mirror). EcID associates to each prediction a specifically developed confidence score. The two main features that make EcID different from other systems are the combination of co-evolution-based predictions with the experimental data, and the introduction of E. coli-specific information, such as gene regulation information from EcoCyc. The possibilities offered by the combination of the EcID database information are illustrated with a prediction of potential functions for a group of poorly characterized genes related to yeaG. EcID is available online at http://ecid.bioinfo.cnio.es.
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影响因子：
14.9
作者：
Kanehisa M;Araki M;Goto S;Hattori M;Hirakawa M;Itoh M;Katayama T;Kawashima S;Okuda S;Tokimatsu T;Yamanishi Y
通讯作者：
Yamanishi Y
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3.2
作者：
Ibanez-Ruiz, M;Robbe-Saule, V;Norel, F
通讯作者：
Norel, F
影响因子：
14.9
作者：
Kersey, P;Bower, L;Apweiler, R
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Apweiler, R
影响因子：
13.8
作者：
Dandekar, T;Snel, B;Bork, P
通讯作者：
Bork, P
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