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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
Screenshot of the main page of HTRIdb. Through the buttons in the left menu, users can access all HTRIdb features. To search TF-TG interactions data of interest, users should click the “SEARCH” button. To keep track of the number of TFs, TGs, TF-TG interactions, articles and techniques present in HTRIdb and verify the proportion of known human TFs covered by HTRIdb, users should click the“STATISTICS” button. To download all interactions–TF-TG or TF-TG with PPIs–users should click the “DOWNLOAD” button. To learn how to retrieve and download or visualize as a network the TF-TG interactions and PPIs of a given TF or TG of interest, users should click the “TUTORIAL” button. To add new TF-TG interaction data to HTRIdb by uploading their newly discovered TF-TG interactions data, users should click the “UPLOAD DATA” button. To send suggestions and comments or point out inconsistencies encountered in some TF-TG interaction to HTRIdb staff, users should click the “CONTACT US” button.
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Related In: Results  -  Collection

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Figure 2: Screenshot of the main page of HTRIdb. Through the buttons in the left menu, users can access all HTRIdb features. To search TF-TG interactions data of interest, users should click the “SEARCH” button. To keep track of the number of TFs, TGs, TF-TG interactions, articles and techniques present in HTRIdb and verify the proportion of known human TFs covered by HTRIdb, users should click the“STATISTICS” button. To download all interactions–TF-TG or TF-TG with PPIs–users should click the “DOWNLOAD” button. To learn how to retrieve and download or visualize as a network the TF-TG interactions and PPIs of a given TF or TG of interest, users should click the “TUTORIAL” button. To add new TF-TG interaction data to HTRIdb by uploading their newly discovered TF-TG interactions data, users should click the “UPLOAD DATA” button. To send suggestions and comments or point out inconsistencies encountered in some TF-TG interaction to HTRIdb staff, users should click the “CONTACT US” button.

Mentions: The 51871 TF-TG interactions currently present in HTRIdb is certainly much lower than the amount of existing TF-TG interactions in human. Therefore, to increase the number of TF-TG interactions in HTRIdb, we plan to update it periodically by manually curating the literature. Also, and more importantly: researchers involved in transcriptional regulatory studies can contribute to HTRIdb by uploading their newly discovered TF-TG interactions data via the “Upload Data” page accessible from the main page of HTRIdb (see Figure 2).


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

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

Screenshot of the main page of HTRIdb. Through the buttons in the left menu, users can access all HTRIdb features. To search TF-TG interactions data of interest, users should click the “SEARCH” button. To keep track of the number of TFs, TGs, TF-TG interactions, articles and techniques present in HTRIdb and verify the proportion of known human TFs covered by HTRIdb, users should click the“STATISTICS” button. To download all interactions–TF-TG or TF-TG with PPIs–users should click the “DOWNLOAD” button. To learn how to retrieve and download or visualize as a network the TF-TG interactions and PPIs of a given TF or TG of interest, users should click the “TUTORIAL” button. To add new TF-TG interaction data to HTRIdb by uploading their newly discovered TF-TG interactions data, users should click the “UPLOAD DATA” button. To send suggestions and comments or point out inconsistencies encountered in some TF-TG interaction to HTRIdb staff, users should click the “CONTACT US” button.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 2: Screenshot of the main page of HTRIdb. Through the buttons in the left menu, users can access all HTRIdb features. To search TF-TG interactions data of interest, users should click the “SEARCH” button. To keep track of the number of TFs, TGs, TF-TG interactions, articles and techniques present in HTRIdb and verify the proportion of known human TFs covered by HTRIdb, users should click the“STATISTICS” button. To download all interactions–TF-TG or TF-TG with PPIs–users should click the “DOWNLOAD” button. To learn how to retrieve and download or visualize as a network the TF-TG interactions and PPIs of a given TF or TG of interest, users should click the “TUTORIAL” button. To add new TF-TG interaction data to HTRIdb by uploading their newly discovered TF-TG interactions data, users should click the “UPLOAD DATA” button. To send suggestions and comments or point out inconsistencies encountered in some TF-TG interaction to HTRIdb staff, users should click the “CONTACT US” button.
Mentions: The 51871 TF-TG interactions currently present in HTRIdb is certainly much lower than the amount of existing TF-TG interactions in human. Therefore, to increase the number of TF-TG interactions in HTRIdb, we plan to update it periodically by manually curating the literature. Also, and more importantly: researchers involved in transcriptional regulatory studies can contribute to HTRIdb by uploading their newly discovered TF-TG interactions data via the “Upload Data” page accessible from the main page of HTRIdb (see Figure 2).

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