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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
Entity relationship diagram showing the schema for the HTRIdb. The attribute “name” associated with the entities “Transcription Factor” , “Target Gene” and “Protein” represents the gene official symbols for, respectively, a TF, a TG and a TF/TG interacting protein. The attribute “name” associated with “Alias” represents the alias symbol for a TG or a TF. The attribute “name” associated with “Technique” represents a technique name. The attribute “info” represents the TFs’ and TGs’ links to their respective Entrez Gene report pages. The attribute “code” associated with entities “Alias”, “References” and “Techniques” represents an internal code specific for each entity; the attribute “code” associated with entity “Protein” represents the Entrez Gene ID of a TF/TG interacting protein.
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Figure 1: Entity relationship diagram showing the schema for the HTRIdb. The attribute “name” associated with the entities “Transcription Factor” , “Target Gene” and “Protein” represents the gene official symbols for, respectively, a TF, a TG and a TF/TG interacting protein. The attribute “name” associated with “Alias” represents the alias symbol for a TG or a TF. The attribute “name” associated with “Technique” represents a technique name. The attribute “info” represents the TFs’ and TGs’ links to their respective Entrez Gene report pages. The attribute “code” associated with entities “Alias”, “References” and “Techniques” represents an internal code specific for each entity; the attribute “code” associated with entity “Protein” represents the Entrez Gene ID of a TF/TG interacting protein.

Mentions: The HTRIdb provides for each TF-TG interaction (1) the TF and TG gene official and alias symbols, (2) the Entrez Gene ID codes for both TF and TG, (3) links to the Entrez Gene report pages for both TF and TG, (4) the experimental technique used to detect the TF-TG interaction, (5) the Pubmed ID for the article reporting the interaction with a link to the respective article’s abstract page in Pubmed and (6) the protein-protein interactions (PPIs) of both TF and TG. Figure 1 shows the entity relationship diagram depicting the schema for the HTRIdb.


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

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

Entity relationship diagram showing the schema for the HTRIdb. The attribute “name” associated with the entities “Transcription Factor” , “Target Gene” and “Protein” represents the gene official symbols for, respectively, a TF, a TG and a TF/TG interacting protein. The attribute “name” associated with “Alias” represents the alias symbol for a TG or a TF. The attribute “name” associated with “Technique” represents a technique name. The attribute “info” represents the TFs’ and TGs’ links to their respective Entrez Gene report pages. The attribute “code” associated with entities “Alias”, “References” and “Techniques” represents an internal code specific for each entity; the attribute “code” associated with entity “Protein” represents the Entrez Gene ID of a TF/TG interacting protein.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 1: Entity relationship diagram showing the schema for the HTRIdb. The attribute “name” associated with the entities “Transcription Factor” , “Target Gene” and “Protein” represents the gene official symbols for, respectively, a TF, a TG and a TF/TG interacting protein. The attribute “name” associated with “Alias” represents the alias symbol for a TG or a TF. The attribute “name” associated with “Technique” represents a technique name. The attribute “info” represents the TFs’ and TGs’ links to their respective Entrez Gene report pages. The attribute “code” associated with entities “Alias”, “References” and “Techniques” represents an internal code specific for each entity; the attribute “code” associated with entity “Protein” represents the Entrez Gene ID of a TF/TG interacting protein.
Mentions: The HTRIdb provides for each TF-TG interaction (1) the TF and TG gene official and alias symbols, (2) the Entrez Gene ID codes for both TF and TG, (3) links to the Entrez Gene report pages for both TF and TG, (4) the experimental technique used to detect the TF-TG interaction, (5) the Pubmed ID for the article reporting the interaction with a link to the respective article’s abstract page in Pubmed and (6) the protein-protein interactions (PPIs) of both TF and TG. Figure 1 shows the entity relationship diagram depicting the schema for the HTRIdb.

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