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首页> 外文期刊>BMC Genomics >RegPrecise 3.0 – A resource for genome-scale exploration of transcriptional regulation in bacteria
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RegPrecise 3.0 – A resource for genome-scale exploration of transcriptional regulation in bacteria

机译：RegPrecise 3.0 –用于细菌转录调控的基因组规模探索的资源

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Background Genome-scale prediction of gene regulation and reconstruction of transcriptional regulatory networks in prokaryotes is one of the critical tasks of modern genomics. Bacteria from different taxonomic groups, whose lifestyles and natural environments are substantially different, possess highly diverged transcriptional regulatory networks. The comparative genomics approaches are useful for in silico reconstruction of bacterial regulons and networks operated by both transcription factors (TFs) and RNA regulatory elements (riboswitches). Description RegPrecise ( http://regprecise.lbl.gov ) is a web resource for collection, visualization and analysis of transcriptional regulons reconstructed by comparative genomics. We significantly expanded a reference collection of manually curated regulons we introduced earlier. RegPrecise 3.0 provides access to inferred regulatory interactions organized by phylogenetic, structural and functional properties. Taxonomy-specific collections include 781 TF regulogs inferred in more than 160 genomes representing 14 taxonomic groups of Bacteria. TF-specific collections include regulogs for a selected subset of 40 TFs reconstructed across more than 30 taxonomic lineages. Novel collections of regulons operated by RNA regulatory elements (riboswitches) include near 400 regulogs inferred in 24 bacterial lineages. RegPrecise 3.0 provides four classifications of the reference regulons implemented as controlled vocabularies: 55 TF protein families; 43 RNA motif families; ~150 biological processes or metabolic pathways; and ~200 effectors or environmental signals. Genome-wide visualization of regulatory networks and metabolic pathways covered by the reference regulons are available for all studied genomes. A separate section of RegPrecise 3.0 contains draft regulatory networks in 640 genomes obtained by an conservative propagation of the reference regulons to closely related genomes. Conclusions RegPrecise 3.0 gives access to the transcriptional regulons reconstructed in bacterial genomes. Analytical capabilities include exploration of: regulon content, structure and function; TF binding site motifs; conservation and variations in genome-wide regulatory networks across all taxonomic groups of Bacteria. RegPrecise 3.0 was selected as a core resource on transcriptional regulation of the Department of Energy Systems Biology Knowledgebase, an emerging software and data environment designed to enable researchers to collaboratively generate, test and share new hypotheses about gene and protein functions, perform large-scale analyses, and model interactions in microbes, plants, and their communities.
机译：背景技术原核生物中基因调控的基因组规模预测和转录调控网络的重建是现代基因组学的关键任务之一。来自不同分类组的细菌，其生活方式和自然环境有很大不同，它们具有高度不同的转录调控网络。比较基因组学方法可用于计算机重建细菌转录因子和由转录因子（TFs）和RNA调控元件（riboswitches）操纵的网络。描述RegPrecise（http://regprecise.lbl.gov）是一个网络资源，用于收集，可视化和分析通过比较基因组学重建的转录调控子。我们极大地扩展了我们先前介绍的手动管理的regulon的参考集合。 RegPrecise 3.0提供了对通过系统发育，结构和功能特性组织的推断调控相互作用的访问。特定分类学的集合包括从代表14个细菌分类组的160多个基因组中推断出的781个TF regulog。特定于TF的集合包括针对30多个分类谱系重建的40个TF的选定子集的重新记录。由RNA调控元件（核糖开关）操纵的调节子的新集合包括在24个细菌谱系中推断的近400个调节子。 RegPrecise 3.0提供了作为受控词汇表实现的参考规则的四个分类：55个TF蛋白家族; 43个RNA基序家族;约150个生物过程或代谢途径;和约200个效应器或环境信号。全基因组范围内的可视化参考基因调控网络和代谢途径的可视化可用于所有研究的基因组。 RegPrecise 3.0的单独部分包含640个基因组的调控网络草案，这些网络是通过将参考基因组保守地繁殖到密切相关的基因组而获得的。结论RegPrecise 3.0可以访问细菌基因组中重建的转录调控子。分析能力包括探索：法规的内容，结构和功能; TF结合位点基序;所有细菌分类学类别的全基因组调控网络的保护和变异。 RegPrecise 3.0被选为能源系统生物学系知识库的转录调控核心资源，这是一种新兴的软件和数据环境，旨在使研究人员能够协作生成，测试和共享有关基因和蛋白质功能的新假设，进行大规模分析，并模拟微生物，植物及其群落之间的相互作用。

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