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

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.

[1]  Andrey N. Naumochkin,et al.  Transcription Regulatory Regions Database (TRRD): its status in 2002 , 2002, Nucleic Acids Res..

[2]  Albertha J. M. Walhout,et al.  Unraveling transcription regulatory networks by protein-DNA and protein-protein interaction mapping. , 2006, Genome research.

[3]  Alexander E. Kel,et al.  TRANSFAC® and its module TRANSCompel®: transcriptional gene regulation in eukaryotes , 2005, Nucleic Acids Res..

[4]  Michael Q. Zhang,et al.  TRED: a transcriptional regulatory element database, new entries and other development , 2007, Nucleic Acids Res..

[5]  Erik van Nimwegen,et al.  SwissRegulon: a database of genome-wide annotations of regulatory sites , 2006, Nucleic Acids Res..

[6]  Obi L. Griffith,et al.  ORegAnno: an open-access community-driven resource for regulatory annotation , 2007, Nucleic Acids Res..

[7]  IN Actinobacteria.  BIOINFORMATICS ANALYSIS OF PHOH FUNCTION AND REGULATION IN ACTINOBACTERIA , 2008 .

[8]  Juan M. Vaquerizas,et al.  A census of human transcription factors: function, expression and evolution , 2009, Nature Reviews Genetics.

[9]  P.A.C.R. Costa,et al.  A machine learning approach for genome-wide prediction of morbid and druggable human genes based on systems-level data , 2010, BMC Genomics.

[10]  Gary D. Bader,et al.  Cytoscape Web: an interactive web-based network browser , 2010, Bioinform..

[11]  David J. Arenillas,et al.  JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles , 2009, Nucleic Acids Res..

[12]  Li Chen,et al.  hmChIP: a database and web server for exploring publicly available human and mouse ChIP-seq and ChIP-chip data , 2011, Bioinform..

[13]  Ney Lemke,et al.  HTRIdb: an open-access database for experimentally verified human transcriptional regulation interactions , 2012 .