RegPrecise: a database of curated genomic inferences of transcriptional regulatory interactions in prokaryotes.
RegPrecise: a database of curated genomic inferences of transcriptional regulatory interactions in prokaryotes.
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DOI：
10.1093/nar/gkp894
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发表时间：
2010-01
影响因子：
14.9
通讯作者：
Rodionov DA
中科院分区：
文献类型：
--
作者：
Novichkov PS;Laikova ON;Novichkova ES;Gelfand MS;Arkin AP;Dubchak I;Rodionov DA
开发RegPrecise数据库（http：regprecise.lbl.gov）用于捕获、可视化和分析原核生物中预测的转录因子调节子，所述调节子通过利用比较基因组方法重建和手动管理。大量的高质量的转录调控相互作用的推断已经积累了不同的分类群的细菌。重建的调节子包括转录因子、它们的同源DNA基序和与候选转录因子结合位点连接的调节基因/操纵子。RegPrecise允许浏览调节子集合：（i）不同分类谱系中特定调节子的DNA结合位点和受调节基因的保护;（ii）转录因子家族的调节子集;（iii）特定物种分类组中的调节子库;（iv）与各种基因组中的代谢途径或生物过程相关的调节子。该数据库的初始版本包括来自350多个原核基因组的约400个转录因子的邻位组的约11500个候选结合位点。这些数据中的大部分由希瓦氏菌属和链球菌属的全基因组调节子重建和LacI家族转录因子的调节子的大规模预测表示。数据库中的另一部分代表了精确的调节子传播到密切相关的基因组的结果。
The RegPrecise database (http://regprecise.lbl.gov) was developed for capturing, visualization and analysis of predicted transcription factor regulons in prokaryotes that were reconstructed and manually curated by utilizing the comparative genomic approach. A significant number of high-quality inferences of transcriptional regulatory interactions have been already accumulated for diverse taxonomic groups of bacteria. The reconstructed regulons include transcription factors, their cognate DNA motifs and regulated genes/operons linked to the candidate transcription factor binding sites. The RegPrecise allows for browsing the regulon collections for: (i) conservation of DNA binding sites and regulated genes for a particular regulon across diverse taxonomic lineages; (ii) sets of regulons for a family of transcription factors; (iii) repertoire of regulons in a particular taxonomic group of species; (iv) regulons associated with a metabolic pathway or a biological process in various genomes. The initial release of the database includes ∼11 500 candidate binding sites for ∼400 orthologous groups of transcription factors from over 350 prokaryotic genomes. Majority of these data are represented by genome-wide regulon reconstructions in Shewanella and Streptococcus genera and a large-scale prediction of regulons for the LacI family of transcription factors. Another section in the database represents the results of accurate regulon propagation to the closely related genomes.
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影响因子：
14.9
作者：
Krawczyk J;Kohl TA;Goesmann A;Kalinowski J;Baumbach J
通讯作者：
Baumbach J
DOI：
10.1073/pnas.1733691100
发表时间：
2003-08-19
影响因子：
11.1
作者：
Panina, EM;Mironov, AA;Gelfand, MS
通讯作者：
Gelfand, MS
影响因子：
7
作者：
Alm, EJ;Huang, KH;Arkin, AP
通讯作者：
Arkin, AP
影响因子：
4.2
作者：
Permina EA;Kazakov AE;Kalinina OV;Gelfand MS
通讯作者：
Gelfand MS
影响因子：
3
作者：
Baumbach J
通讯作者：
Baumbach J