Volume 12 Supplement 11

Highlights from the Seventh International Society for Computational Biology (ISCB) Student Council Symposium 2011

Open Access

The development of an open-access database for human transcriptional regulation interactions

  • Luiz Augusto Bovolenta1Email author,
  • Marcio Luis Acencio1 and
  • Ney Lemke1
BMC Bioinformatics201112(Suppl 11):A10

DOI: 10.1186/1471-2105-12-S11-A10

Published: 21 November 2011


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 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, such as TRANSFAC [1] and TRED [2]. In an effort to provide researchers with a repository of TF-TG interactions from which such interactions can be directly extracted, we present here the human transcriptional regulation interactions database (HTRIdb), an open-access database of experimentally validated interactions among human TFs and their respective TGs.

Materials and methods

The HTRIdb is implemented as a relational database PostgreSQL that is connected to a web interface via the JBOSS AS application server that dynamically generates user-friendly HTML front-end queries using the Apache Tomcat web server. For the visualization of TF-TG interactions, we embedded in the HTRIdb the Cytoscape Web.


The HTRIdb offers several mechanisms of data query and extraction, such as download in spreadsheet or text format and the visualization of TF-TG interactions. There is an update mechanism that allows scientists to send new data. The HTRIdb currently holds a collection of 2,114 unique transcriptional regulation interactions among 163 TFs and 1,034 TGs.


HTRIdb is a powerful user-friendly tool from which human TF-TG interactions can be easily extracted.



We would like to thank The State of São Paulo Research Foundation (FAPESP) (grants 2009/10382-2 and 2010/20684-3) and CNPQ for the financial support.

Authors’ Affiliations

Department of Physics and Biophysics, Instituto de Biociências de Botucatu, Unesp -Univ Estadual Paulista


  1. Matys V, Kel-Margoulis OV, Fricke E, Liebich I, Land S, Barre-Dirrie A, Reuter I, Chekmenev D, Krull M, Hornischer K, et al.: TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes. Nucleic Acids Res 2006, 34(Database):D108–110.PubMed CentralView ArticlePubMedGoogle Scholar
  2. Jiang C, Xuan Z, Zhao F, Zhang MQ: TRED: a transcriptional regulatory element database, new entries and other development. Nucleic Acids Res 2007, 35(Database):D137–140. 10.1093/nar/gkl1041PubMed CentralView ArticlePubMedGoogle Scholar


© Bovolenta et al; licensee BioMed Central Ltd. 2011

This article is published under license to BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.