RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more.
RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more.
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DOI：
10.1093/nar/gks1201
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发表时间：
2013-01
影响因子：
14.9
通讯作者：
Collado-Vides J
中科院分区：
文献类型：
--
作者：
Salgado H;Peralta-Gil M;Gama-Castro S;Santos-Zavaleta A;Muñiz-Rascado L;García-Sotelo JS;Weiss V;Solano-Lira H;Martínez-Flores I;Medina-Rivera A;Salgado-Osorio G;Alquicira-Hernández S;Alquicira-Hernández K;López-Fuentes A;Porrón-Sotelo L;Huerta AM;Bonavides-Martínez C;Balderas-Martínez YI;Pannier L;Olvera M;Labastida A;Jiménez-Jacinto V;Vega-Alvarado L;Del Moral-Chávez V;Hernández-Alvarez A;Morett E;Collado-Vides J
本文总结了我们在过去两年中对RegulonDB（http://regulondb.ccg.unam.mx/）所取得的进展。我们不断更新已发表文献中有关大肠杆菌K - 12转录调控的知识。我们一直维持并扩大我们的整理工作，以提高所编码实验知识的广度和质量，并且我们已经为计算预测的质量制定了标准。调控短语现在能够对调控区域进行高级描述。我们扩大了对各种证据来源的质量评定，特别是针对通过高通量（HT）技术产生的知识。基于我们对大多数相关方法的分析，当多个独立来源支持一个条目时，我们定义了确定证据质量的规则。随着RegulonDB的这次最新发布，我们展示了一个新的、可靠性更高且规模更大的转录起始位点集合，这是我们在全基因组范围内进行高通量实验的结果。这些改进以及一些新的增强功能（轨迹显示、上传格式和整理指南），解决了将高通量产生的知识纳入RegulonDB所面临的挑战。有关调控元件进化保守性的信息现在也可获取。总之，RegulonDB 8.0版是一个更好的整合现有信息来源中基因调控知识的平台。
This article summarizes our progress with RegulonDB (http://regulondb.ccg.unam.mx/) during the past 2 years. We have kept up-to-date the knowledge from the published literature regarding transcriptional regulation in Escherichia coli K-12. We have maintained and expanded our curation efforts to improve the breadth and quality of the encoded experimental knowledge, and we have implemented criteria for the quality of our computational predictions. Regulatory phrases now provide high-level descriptions of regulatory regions. We expanded the assignment of quality to various sources of evidence, particularly for knowledge generated through high-throughput (HT) technology. Based on our analysis of most relevant methods, we defined rules for determining the quality of evidence when multiple independent sources support an entry. With this latest release of RegulonDB, we present a new highly reliable larger collection of transcription start sites, a result of our experimental HT genome-wide efforts. These improvements, together with several novel enhancements (the tracks display, uploading format and curational guidelines), address the challenges of incorporating HT-generated knowledge into RegulonDB. Information on the evolutionary conservation of regulatory elements is also available now. Altogether, RegulonDB version 8.0 is a much better home for integrating knowledge on gene regulation from the sources of information currently available.
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影响因子：
14.9
作者：
Łyzen R;Kochanowska M;Wegrzyn G;Szalewska-Palasz A
通讯作者：
Szalewska-Palasz A
影响因子：
--
作者：
Karatza, P;Frillingos, S
通讯作者：
Frillingos, S
影响因子：
--
作者：
Donlin, Maureen J
通讯作者：
Donlin, Maureen J
影响因子：
14.9
作者：
Keseler IM;Collado-Vides J;Santos-Zavaleta A;Peralta-Gil M;Gama-Castro S;Muñiz-Rascado L;Bonavides-Martinez C;Paley S;Krummenacker M;Altman T;Kaipa P;Spaulding A;Pacheco J;Latendresse M;Fulcher C;Sarker M;Shearer AG;Mackie A;Paulsen I;Gunsalus RP;Karp PD
通讯作者：
Karp PD
影响因子：
5.6
作者：
Belyaeva, TA;Rhodius, VA;Busby, SJW
通讯作者：
Busby, SJW