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

BMC Genomics

Database

Ney Lemke¹  Marcio L Acencio¹  Luiz A Bovolenta¹ 

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

关键词: Chromatin Immunoprecipitation;    Transcriptional Regulatory Network;    Result Page;    Respective Target Gene;    Transcriptional Regulation Interaction;   

DOI  :  10.1186/1471-2164-13-405

 received in 2012-04-26, accepted in 2012-07-20,  发布年份 2012

来源: Springer

【 摘 要 】

BackgroundThe 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).DescriptionThe 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.ConclusionsHTRIdb 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.

【 授权许可】

CC BY   
© Bovolenta et al.; licensee BioMed Central Ltd. 2012