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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 network visualization pages. This tool is provided by the embedded Cytoscape Web software [5] and shows networks in three levels: first level displays only the interactions between the TF of interest and its TGs (A), second level displays interactions from first level plus PPIs between TF of interest and other proteins (B) and third level displays interaction from first and second level plus PPIs between TGs and other proteins (C).
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Figure 7: Screenshots of the network visualization pages. This tool is provided by the embedded Cytoscape Web software [5] and shows networks in three levels: first level displays only the interactions between the TF of interest and its TGs (A), second level displays interactions from first level plus PPIs between TF of interest and other proteins (B) and third level displays interaction from first and second level plus PPIs between TGs and other proteins (C).

Mentions: In the network visualization tool provided by the embedded Cytoscape Web software [8], networks can be seen in three levels (Figure 7). The first level displays only the interactions between the TF of interest and its TGs (Figure 7a), the second level displays interactions from first level plus PPIs between TF of interest and other proteins (Figure 7b) and the third level displays interaction from first and second levels plus PPIs between TGs and other proteins (Figure 7c). The network displayed in the second and third levels can be downloaded in text format by clicking the“Download Network” icon (Figures 7b and 7c).


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

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

Screenshots of the network visualization pages. This tool is provided by the embedded Cytoscape Web software [5] and shows networks in three levels: first level displays only the interactions between the TF of interest and its TGs (A), second level displays interactions from first level plus PPIs between TF of interest and other proteins (B) and third level displays interaction from first and second level plus PPIs between TGs and other proteins (C).
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 7: Screenshots of the network visualization pages. This tool is provided by the embedded Cytoscape Web software [5] and shows networks in three levels: first level displays only the interactions between the TF of interest and its TGs (A), second level displays interactions from first level plus PPIs between TF of interest and other proteins (B) and third level displays interaction from first and second level plus PPIs between TGs and other proteins (C).
Mentions: In the network visualization tool provided by the embedded Cytoscape Web software [8], networks can be seen in three levels (Figure 7). The first level displays only the interactions between the TF of interest and its TGs (Figure 7a), the second level displays interactions from first level plus PPIs between TF of interest and other proteins (Figure 7b) and the third level displays interaction from first and second levels plus PPIs between TGs and other proteins (Figure 7c). The network displayed in the second and third levels can be downloaded in text format by clicking the“Download Network” icon (Figures 7b and 7c).

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