CollecTF: a database of experimentally validated transcription factor-binding sites in Bacteria.
CollecTF: a database of experimentally validated transcription factor-binding sites in Bacteria.
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DOI：
10.1093/nar/gkt1123
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发表时间：
2014-01
影响因子：
14.9
通讯作者：
Erill I
中科院分区：
文献类型：
--
作者：
Kiliç S;White ER;Sagitova DM;Cornish JP;Erill I
高通量数据的涌入和复杂的模型来描述原核转录因子（TF）与其靶位点的相互作用的需要，对TF结合位点数据库提出了新的挑战。CollectTF（collectf.umbc.edu）汇编了实验验证的、细菌域中天然存在的TF结合位点的数据，非常强调策展过程的透明度、存储数据的质量和可用性以及对其记录的完全可定制访问。CollecTF自动开放地集成了多个数据源，允许用户动态地重新定义绑定基序及其实验支持基础。CollecTF通过采用可持续的模式来促进数据质量和流通性，该模式鼓励作者直接提交，并结合对已发表文献的内部验证和管理。CollectTF条目定期提交给NCBI，以整合到RefSeq完整基因组记录中作为链接功能，最大限度地提高数据的可见性并丰富RefSeq文件的注释与监管信息。为了促进调控相互作用的比较基因组学和机器学习分析，在其初始版本中，CollectTF提供了两个TF家族（莱克萨和Fur）的全域覆盖，以及临床重要细菌家族弧菌科的广泛代表性。
The influx of high-throughput data and the need for complex models to describe the interaction of prokaryotic transcription factors (TF) with their target sites pose new challenges for TF-binding site databases. CollecTF (http://collectf.umbc.edu) compiles data on experimentally validated, naturally occurring TF-binding sites across the Bacteria domain, placing a strong emphasis on the transparency of the curation process, the quality and availability of the stored data and fully customizable access to its records. CollecTF integrates multiple sources of data automatically and openly, allowing users to dynamically redefine binding motifs and their experimental support base. Data quality and currency are fostered in CollecTF by adopting a sustainable model that encourages direct author submissions in combination with in-house validation and curation of published literature. CollecTF entries are periodically submitted to NCBI for integration into RefSeq complete genome records as link-out features, maximizing the visibility of the data and enriching the annotation of RefSeq files with regulatory information. Seeking to facilitate comparative genomics and machine-learning analyses of regulatory interactions, in its initial release CollecTF provides domain-wide coverage of two TF families (LexA and Fur), as well as extensive representation for a clinically important bacterial family, the Vibrionaceae.
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影响因子：
14.9
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
通讯作者：
Collado-Vides J
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影响因子：
14.9
作者：
Mahony, Shaun;Benos, Panayiotis V
通讯作者：
Benos, Panayiotis V
影响因子：
14.9
作者：
Pauling J;Röttger R;Tauch A;Azevedo V;Baumbach J
通讯作者：
Baumbach J
影响因子：
4.2
作者：
Paul, Ligi;Mishra, Pankaj K.;Matthews, Rowena G.
通讯作者：
Matthews, Rowena G.
Oreganno：一种开放访问社区驱动的监管注释资源。
影响因子：
14.9
作者：
Griffith OL;Montgomery SB;Bernier B;Chu B;Kasaian K;Aerts S;Mahony S;Sleumer MC;Bilenky M;Haeussler M;Griffith M;Gallo SM;Giardine B;Hooghe B;Van Loo P;Blanco E;Ticoll A;Lithwick S;Portales-Casamar E;Donaldson IJ;Robertson G;Wadelius C;De Bleser P;Vlieghe D;Halfon MS;Wasserman W;Hardison R;Bergman CM;Jones SJ;Open Regulatory Annotation Consortium
通讯作者：
Open Regulatory Annotation Consortium