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

Bovolenta LA, Acencio ML, Lemke N - BMC Genomics (2012)

Bottom Line: 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.

View Article: PubMed Central - HTML - PubMed

Affiliation: 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. labovolenta@ibb.unesp.br

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.

Show MeSH
Screenshots of the result pages of HTRIdb, TRED and ORegAnno. The result page of HTRIdb displays all TF-TG interactions data in one page only (A), while the result pages of TRED (B) and ORegAnno (C) show partial TF-TG interactions data and are broken into subpages.
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Figure 8: Screenshots of the result pages of HTRIdb, TRED and ORegAnno. The result page of HTRIdb displays all TF-TG interactions data in one page only (A), while the result pages of TRED (B) and ORegAnno (C) show partial TF-TG interactions data and are broken into subpages.

Mentions: TRED and TRRD are freely accessible as HTRIdb is, but their major drawback is that they do not provide links to download their collection of TF-TG interactions. Conversely, HTRIdb, besides providing links to download the displayed results (Figure 6), also provides links to download all TF-TG interactions through the “DOWNLOAD” page that is easily accessible from the main page of HTRIdb (Figure 2). Besides the presence of download links, HTRIdb also offers additional advantages over TRED and TRRD, such as a dynamic network visualization tool, which is absent in TRRD and TRED (in fact, TRED provides only static images showing the interactions), and a more friendly result page. While the result page of TRED is broken into subpages containing a maximum of 20 TGs each in which techniques and Pubmed IDs are not displayed (Figure 8b), the result page of HTRIdb displays all TGs of the TF of interest along with the techniques used to detect the interactions and the Pubmed IDs for articles reporting the interactions (Figure 6 and Figure 8a). Regarding the result page of TRRD, links to pages showing further information on TF-TG interactions of interest are all displayed at once, but the names of links are non-obvious internal identifiers used by TRRD.


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

Bovolenta LA, Acencio ML, Lemke N - BMC Genomics (2012)

Screenshots of the result pages of HTRIdb, TRED and ORegAnno. The result page of HTRIdb displays all TF-TG interactions data in one page only (A), while the result pages of TRED (B) and ORegAnno (C) show partial TF-TG interactions data and are broken into subpages.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3472291&req=5

Figure 8: Screenshots of the result pages of HTRIdb, TRED and ORegAnno. The result page of HTRIdb displays all TF-TG interactions data in one page only (A), while the result pages of TRED (B) and ORegAnno (C) show partial TF-TG interactions data and are broken into subpages.
Mentions: TRED and TRRD are freely accessible as HTRIdb is, but their major drawback is that they do not provide links to download their collection of TF-TG interactions. Conversely, HTRIdb, besides providing links to download the displayed results (Figure 6), also provides links to download all TF-TG interactions through the “DOWNLOAD” page that is easily accessible from the main page of HTRIdb (Figure 2). Besides the presence of download links, HTRIdb also offers additional advantages over TRED and TRRD, such as a dynamic network visualization tool, which is absent in TRRD and TRED (in fact, TRED provides only static images showing the interactions), and a more friendly result page. While the result page of TRED is broken into subpages containing a maximum of 20 TGs each in which techniques and Pubmed IDs are not displayed (Figure 8b), the result page of HTRIdb displays all TGs of the TF of interest along with the techniques used to detect the interactions and the Pubmed IDs for articles reporting the interactions (Figure 6 and Figure 8a). Regarding the result page of TRRD, links to pages showing further information on TF-TG interactions of interest are all displayed at once, but the names of links are non-obvious internal identifiers used by TRRD.

Bottom Line: 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.

View Article: PubMed Central - HTML - PubMed

Affiliation: 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. labovolenta@ibb.unesp.br

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.

Show MeSH