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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 “Transcription Factor” page within “Search” page. In this page, users should select the type of search key. If they know the TF’s EntrezGene ID, the “NCBI GeneID” option should be selected and the desired EntrezGene ID should be entered in the search field; otherwise, the “Gene Symbol” option should be selected and the complete or partial TF’s official gene or alias symbol should be entered in the search field. In this case, the user entered the TF’s gene partial symbol “PAX”.
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Figure 4: Screenshot of the “Transcription Factor” page within “Search” page. In this page, users should select the type of search key. If they know the TF’s EntrezGene ID, the “NCBI GeneID” option should be selected and the desired EntrezGene ID should be entered in the search field; otherwise, the “Gene Symbol” option should be selected and the complete or partial TF’s official gene or alias symbol should be entered in the search field. In this case, the user entered the TF’s gene partial symbol “PAX”.

Mentions: Regarding the search mechanism (for a simple use case, please see the next section), users can retrieve TF-TG interactions data on a specific TF or TG of interest. For this purpose, users should access the “SEARCH” page and then proceed to the “TRANSCRIPTION FACTOR” or to the “TARGET GENE” page, depending on the type of search (Figure 3). In these pages, queries can be entered using the Entrez Gene ID code or the total or partial TF or TG gene official or alias symbols (Figure 4). This feature eliminates the need for users to know the exact name of TF or TG of interest; moreover, a page containing a list of possible TF or TG gene official symbols matching the entered query further helps users to confirm their choice (Figure 5). The retrieved data includes the Entrez Gene IDs, the gene official symbols and the links to the respective Entrez Gene report pages for both TFs and TGs and the name of experimental technique used to detect the interactions with the Pubmed IDs for articles reporting the discovery of these interactions (Figure 6). TF-TG interactions data only or TF-TG interactions data associated with their PPIs can be downloaded in a tab-delimited or spreadsheet file; moreover, TF-TG interactions can be visualized as a network by clicking the “Graph” icon (Figure 6).


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

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

Screenshot of the “Transcription Factor” page within “Search” page. In this page, users should select the type of search key. If they know the TF’s EntrezGene ID, the “NCBI GeneID” option should be selected and the desired EntrezGene ID should be entered in the search field; otherwise, the “Gene Symbol” option should be selected and the complete or partial TF’s official gene or alias symbol should be entered in the search field. In this case, the user entered the TF’s gene partial symbol “PAX”.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 4: Screenshot of the “Transcription Factor” page within “Search” page. In this page, users should select the type of search key. If they know the TF’s EntrezGene ID, the “NCBI GeneID” option should be selected and the desired EntrezGene ID should be entered in the search field; otherwise, the “Gene Symbol” option should be selected and the complete or partial TF’s official gene or alias symbol should be entered in the search field. In this case, the user entered the TF’s gene partial symbol “PAX”.
Mentions: Regarding the search mechanism (for a simple use case, please see the next section), users can retrieve TF-TG interactions data on a specific TF or TG of interest. For this purpose, users should access the “SEARCH” page and then proceed to the “TRANSCRIPTION FACTOR” or to the “TARGET GENE” page, depending on the type of search (Figure 3). In these pages, queries can be entered using the Entrez Gene ID code or the total or partial TF or TG gene official or alias symbols (Figure 4). This feature eliminates the need for users to know the exact name of TF or TG of interest; moreover, a page containing a list of possible TF or TG gene official symbols matching the entered query further helps users to confirm their choice (Figure 5). The retrieved data includes the Entrez Gene IDs, the gene official symbols and the links to the respective Entrez Gene report pages for both TFs and TGs and the name of experimental technique used to detect the interactions with the Pubmed IDs for articles reporting the discovery of these interactions (Figure 6). TF-TG interactions data only or TF-TG interactions data associated with their PPIs can be downloaded in a tab-delimited or spreadsheet file; moreover, TF-TG interactions can be visualized as a network by clicking the “Graph” icon (Figure 6).

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