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1.
Figure 8

Figure 8. From: HTRIdb: an open-access database for experimentally verified human transcriptional regulation interactions.

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.

Luiz A Bovolenta, et al. BMC Genomics. 2012;13:405-405.
2.
Figure 3

Figure 3. From: HTRIdb: an open-access database for experimentally verified human transcriptional regulation interactions.

Screenshot of the “Search” page. In this page, users should click the “TRANSCRIPTION FACTOR” or the “TARGET GENE” buttons if they want to search TF-TG interactions data for, respectively, a TF or a TG of interest.

Luiz A Bovolenta, et al. BMC Genomics. 2012;13:405-405.
3.
Figure 5

Figure 5. From: HTRIdb: an open-access database for experimentally verified human transcriptional regulation interactions.

Screenshot of the page to select and confirm the TF of interest. This page shows a list of possible TF’s gene official symbols matching the entered query in the “Transcription Factor” page (in this case, “PAX”–see Figure 4). Here, PAX8 was selected by the user as the TF of interest.

Luiz A Bovolenta, et al. BMC Genomics. 2012;13:405-405.
4.
Figure 4

Figure 4. From: HTRIdb: an open-access database for experimentally verified human transcriptional regulation interactions.

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”.

Luiz A Bovolenta, et al. BMC Genomics. 2012;13:405-405.
5.
Figure 7

Figure 7. From: HTRIdb: an open-access database for experimentally verified human transcriptional regulation interactions.

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).

Luiz A Bovolenta, et al. BMC Genomics. 2012;13:405-405.
6.
Figure 1

Figure 1. From: HTRIdb: an open-access database for experimentally verified human transcriptional regulation interactions.

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.

Luiz A Bovolenta, et al. BMC Genomics. 2012;13:405-405.
7.
Figure 6

Figure 6. From: HTRIdb: an open-access database for experimentally verified human transcriptional regulation interactions.

Screenshot of the result page. The result page displays all TF-TG interactions related to the TF of interest (in this case, PAX8). It contains TF’s NCBI GeneID, TF’s official gene symbol, link for additional information on TF in the Entrez Gene database, TG’s NCBI GeneID, TG’s official gene symbol, link for additional information on TG in the Entrez Gene database, the technique used to detect the TF-TG interaction and the link for the Pubmed abstract for the article describing the interaction. Moreover, by clicking the “Graph” or “Download” icons, users can, respectively, visualize the TF-TG interactions as a network or download TF-TG interactions data only or TF-TG interactions data associated with their PPIs in a tab-delimited or spreadsheet file.

Luiz A Bovolenta, et al. BMC Genomics. 2012;13:405-405.
8.
Figure 2

Figure 2. From: HTRIdb: an open-access database for experimentally verified human transcriptional regulation interactions.

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.

Luiz A Bovolenta, et al. BMC Genomics. 2012;13:405-405.

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