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HTRIdb：一个用于实验验证的人类转录调控相互作用的开放获取数据库。

HTRIdb: an open-access database for experimentally verified human transcriptional regulation interactions.

机构信息

Departamento de Física e Biofísica, Instituto de Biociências de Botucatu, Unesp - Univ Estadual Paulista, Distrito de Rubião Jr, s/n, Botucatu, São Paulo, 18618-970, Brazil.

出版信息

BMC Genomics. 2012 Aug 17;13:405. doi: 10.1186/1471-2164-13-405.

DOI:10.1186/1471-2164-13-405
PMID:22900683
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC3472291/
Abstract

BACKGROUND

The modeling of interactions among transcription factors (TFs) and their respective target genes (TGs) into transcriptional regulatory networks is important for the complete understanding of regulation of biological processes. In the case of experimentally verified human TF-TG interactions, there is no database at present that explicitly provides such information even though many databases containing human TF-TG interaction data have been available. In an effort to provide researchers with a repository of experimentally verified human TF-TG interactions from which such interactions can be directly extracted, we present here the Human Transcriptional Regulation Interactions database (HTRIdb).

DESCRIPTION

The HTRIdb is an open-access database that can be searched via a user-friendly web interface and the retrieved TF-TG interactions data and the associated protein-protein interactions can be downloaded or interactively visualized as a network through the web version of the popular Cytoscape visualization tool, the Cytoscape Web. Moreover, users can improve the database quality by uploading their own interactions and indicating inconsistencies in the data. So far, HTRIdb has been populated with 284 TFs that regulate 18302 genes, totaling 51871 TF-TG interactions. HTRIdb is freely available at http://www.lbbc.ibb.unesp.br/htri.

CONCLUSIONS

HTRIdb is a powerful user-friendly tool from which human experimentally validated TF-TG interactions can be easily extracted and used to construct transcriptional regulation interaction networks enabling researchers to decipher the regulation of biological processes.

摘要

背景

将转录因子 (TF) 及其各自的靶基因 (TG) 之间的相互作用建模为转录调控网络对于全面了解生物过程的调控非常重要。在经过实验验证的人类 TF-TG 相互作用的情况下，目前没有专门提供此类信息的数据库，尽管已经有许多包含人类 TF-TG 相互作用数据的数据库。为了为研究人员提供一个可从中直接提取此类相互作用的经过实验验证的人类 TF-TG 相互作用的存储库，我们在此介绍人类转录调控相互作用数据库 (HTRIdb)。

描述

HTRIdb 是一个开放访问的数据库，可以通过用户友好的 Web 界面进行搜索，检索到的 TF-TG 相互作用数据以及相关的蛋白质-蛋白质相互作用可以通过流行的 Cytoscape 可视化工具的 Web 版本 Cytoscape Web 下载或作为网络进行交互式可视化。此外，用户可以通过上传自己的相互作用并指出数据中的不一致来提高数据库的质量。到目前为止，HTRIdb 已经收录了 284 个调节 18302 个基因的 TF，共计 51871 个 TF-TG 相互作用。HTRIdb 可免费在 http://www.lbbc.ibb.unesp.br/htri 获得。

结论

HTRIdb 是一个功能强大的用户友好工具，可从中轻松提取人类经过实验验证的 TF-TG 相互作用，并用于构建转录调控相互作用网络，使研究人员能够破译生物过程的调控。

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