HINTdb Help
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Help Topics

  1. Introduction

  2. Statistics

  3. Search

  4. Search Results

  5. Interaction Results

  6. Interactions

  7. Reference


Introduction

    HINTdb is a protein-protein interaction database which contains interactions from 105 species with their homologs in one or more species. The protein-protein interaction data includes that from small scale as well as high-throughput experiments from IntAct, BioGRID, HPRD, DIP and MINT. The homologous interactions are also derived from these databases. Hence the interactions and their homologs identified by Hintdb are experimentally determined physical protein-protein interactions. None of the interactions in Hintdb are predicted.

   PSI-Blast was used to identify the homologous interactions. KEGG Orthology data was used to identify orthologous and paralogous interactions. Domain information for the proteins was obtained from the InterPro database. Gene Ontology terms have been assigned from the GO database.

    The web interface of HINTdb allows the user to select interactions of a particular protein and to further view the homologs of that interaction.

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Statistics

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Search

    Interactions can be searched for through their interacting proteins. The proteins can be searched for SwissProt entry ID, name or description. It can also be searched by its ID in the source database, eg. protein ID in IntAct.

    To search the interactions for a particular protein, type any of the above attributes in the Search text box and hit the "Search" button. This will take you to the Search Results page which will show a list of proteins. Click on the desired protein, to view its interactions in HINTdb.

    Further selection of an interaction gives all the information about the interaction, the interacting proteins and the interaction homologs.

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Search Results

The Search Results page displays a list of the proteins found in HINTdb with the keyword or the ID that was queried. The results are displayed in a tabular format with the following columns:

  1. Protein : Uniprot ID of the protein containing the searched keyword or ID.

  2. Description: Name and description of the protein

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Interaction Results

The Interaction Results page displays a list of the interactions that were found in HINTdb for the selected protein. The results are displayed in a tabular form with the following columns:

  1. ID: This is the interaction ID in HINTdb. Clicking on it leads you to the Interactions page which gives further information about the interactions and its homologs, if any.

  2. Interactor: Protein which interacts with the query protein.

  3. Interaction Homologs: The number of Homologous interactions found in the database for this interaction.

 If the search results are not what you expected, you can try another search from the top right hand corner of the Results page.

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Interactions

    The Interactions page shows detailed information about the interaction selected from the Results page. This page shows 3 different kinds of information:

  1. Interaction - This gives some basic information about the interaction that was obtained from the source database.

    • ID: The Interaction ID in HINTdb is on the very first line of this page.

    • Interacting Proteins: Names, UniProt IDs and descriptions of the 2 interacting proteins.

    • Species: The species in which the interaction was detected.

    • Source DB: The database from which the information about this interaction was obtained. The interaction can be accessed in its source database by clicking on the link provided.

    • Pubmed ID: The publications associated with the experimental evidence of this interaction. Each publication provides a link to the PubMed site.

    • Identification Method: The experimental method used to detect the interaction.

    • Interaction Type: The type of interaction eg. direct interaction or physical association.

     

  2. Homologous Interactions - Detailed information about the homologous interactions found. If none are found, the "No Homologous Interactions" is printed at the bottom of the page.

    • Graphical View: The graphical view is shown by default for each interaction. A snapshot of the view is given below.

       

      • The first lines shows the legend used to color code the homologs of each of the interacting proteins. The color coding scheme is the same as that used on the BLAST web page at NCBI.

      • The next line represents the query interaction (current interaction) in the form of two yellow bars - each representing the length of the corresponding interacting protein. At the two corners of each bar, the number of the first and last amino acid in the protein sequence are indicated. Holding the cursor on the bar displays the name of the protein in the form of a tool tip. In the leftmost column on this row, the species in which the interaction was found is indicated.

      • This is followed by the InterPro domains found in the proteins, drawn in cyan. The cyan bars in each row represent a single domain found in the protein. The bars in each row are colored over the length of the protein where they are found. Holding the cursor on any of the bars displays the name of the domain and it's start and end along the length of the protein.

      • Next, the list of the homologous interactions are shown. Each row, represents  one homologous interaction, with the two bars being the two proteins that are homologous to each of the two interacting proteins of the query protein. The species in which the interaction is found is shown next to the bars. The colors of the bars are given based on the score of the hit and according to the legend shown above. The + at the beginning of each row can be clicked to display some information about the proteins in the homologous interactions and some PSIBLAST parameters. Holding the cursor on all bars, displays the name of the protein as a tool tip.

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Reference

    Ashwini Patil and Haruki Nakamura; HINT: a database of annotated protein-protein interactions and their homologs, BIOPHYSICS, Vol. 1, pp.21-24 (2005). Abstract

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Human Genome Center, The Institute of Medical Science, The University of Tokyo

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