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

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 humanTF-TG interactions from which such interactions can be directly extracted, we present here the Human Transcriptional Regulation Interactions database (HTRIdb).MethodThe HTRIdb is implemented as a relational database PostgreSQL that is connected to a web interface via the JBOSS AS that dynamically generates user-friendly HTML front-end queries using the Apache Tomcat web server. For the network visualization of interactions, HTRIdb uses the web version of the popular Cytoscape visualization tool (Cytoscape Web).

The TF-TG interactions data currently present in HTRIdb have been collected from original research articles.

Results: 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. 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.

Conclusion: 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.

Author: Luiz A BovolentaMarcio L AcencioNey Lemke
Credits/Source: BMC Genomics 2012, 13:405

Published on: 2012-08-17

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