Summary of the Search page

The purpose of Search is to explore the interactors of the query protein with all their localization data. The search can be Basic Search, Advanced Search or Direct Protein ID Search. We will list the details of these three options below.

Basic Search starts with a form to specify the name of the query protein. The search term can be the full ID or even a fragment of the name of the protein. A list of suggested names pops up after typing at least 3 characters.

Using the Advanced Search option the user may set the filtration of the query protein for the available species and subcellular localizations. Localization score can be set numerically or by moving the slider. The advanced parameters apply only to the query protein, and not to its interactors, but the settings could be inherited to the interactors as well by check in the "Apply all settings to the results page" box. Once the Advanced Search is executed, that (those) version(s) of the query protein will appear on the screen, which fulfill(s) the parameters of the Advanced Search query. The search is permissive and not restrictive, therefore, in the final interaction page of the query protein you may see other localizations or lower localization scores than the customized parameters unless the "Apply all settings to the results page" box is checked in, when the applied setting are inherited to the interactors as well.

If a single protein was found, the page of interactors is shown immediately. If there are multiple search results for a given protein name (or fragment), an intermediate page displays the available options. The final interaction page displays the properties of the query protein and the interactions as well. All interactions contain information about the properties of the interacting partners and the interaction score of a certain interaction.

On the results page the user could filter the interactions by the 6 major subcellular localizations, localization score thresholds and interaction score thresholds of the interacting partners. The export of the protein search results is available in Tab-limited Text format. The downloaded file is appropiate for further manipulation in Excel as well.

Network visualization of the interactome is also available on the results page. The first-neighbour network shows the interaction map after the filtration (if there was any). Edge-widths are proportional to the respective Interaction Score.

A Direct Protein ID Search option is also available using the following URL format: http://comppi.linkgroup.hu/protein_search/{protein ID, such as the requested UniProtKB accesison}. Try this example to explore the interactions of the Polyductin protein: http://comppi.linkgroup.hu/protein_search/P08F94

Visit our Tutorial to learn more about how to use the Search page or move your mouse over any of the Search form elements to display a location-sensitive tooltip.

Properties of the query protein

On the top of the result page the following properties are listed regarding the query protein:

  1. the Full Name of the protein from the UniProt database and link to the UniProt Profile
  2. Custom Settings options to filter the interactions displayed on the results page
  3. the Species for the given query protein
  4. the Number of Interactions gives the number of the existing interactions for the given protein
  5. the Average Interaction Score gives the average of all the interactions for the given protein
  6. the Localizations table contains the following properties for the subcellular localization of the protein:
    • the list of Major Localizations: every entry is in a new row
    • the list of Minor Localizations: if the name of the minor localization was the same like the name of the major localization, then there is no detailed localization information available
    • the Localization Score contains the calculated score for the given major localization. Learn more about the Localization Score here.
    • the Experiment Type column contains the system type of the localization data: experimental, predicted or unknown with more detailed name if it was available
    • the Source Database list contains the source of the entry
    • the PubMed column contains the PubMed ID of the entry, usually the related publication of the source database
    Experimental localizations are highlighted.
  7. the Synonyms of the query protein contain all the protein names stored in the ComPPI database

Properties of the interactions

On the result page the interactions are listed after the box including the properties of the query protein. The following properties are included:

  1. the Interaction Score is available for all the interactions, where both interactors have at least one major localization. If there was no localization information, then the Interaction Score is 0. See more about the Interaction Score here.
  2. the UniProt accession and the Full Name of the interactor protein
  3. the ComPPI Interactors link navigates directly to the interactions of the certain interactor protein
  4. the UniProtKB Profile is directly available for the interactors
  5. the Details show the properties of the interactor protein after clicking. The ALl Details option shows the properties of all interactor proteins.

Properties of the interacting partners

The structure of the properties of the interacting partner is the following:

  1. the Full Name of the protein from the UniProt database and link to the UniProt Profile
  2. the ComPPI Interactors link navigates directly to the interactions of the certain interactor protein
  3. the UniProtKB Profile for the interactors is directly available
  4. the Localizations table contains the following properties for the subcellular localization of the selected protein:
    • the list of Major Localizations: every entry is in a new row
    • the list of Minor Localizations: if the name of the minor localization was the same like the name of the major localization, then there is no detailed localization information available
    • the Localization Score contains the calculated score for the given major localization. See more about the Localization Score here.
    • the Experiment Type column contains the system type of the localization data: experimental, predicted, or unknown with more detailed name if it was available
    • the Source Database list contains the source of the entry
    • the PubMed column contains the PubMed ID of the entry, usually the related publication of the source database
    Experimental localizations are highlighted.
  5. the Synonyms of the query protein contain all the protein names stored in the ComPPI database
  6. the Interaction Source Database lists the source databases for the given interaction
  7. the Interaction Source Publication lists the publications of the sources for the given interaction

Properties of the downloadable data

The structure of the properties of the query protein and its interacting partners is the following:

  1. Interactor: UniProt accession of the query protein in the first rao, and of its interactors in the following rows
  2. Canonical Name: UniProt full and short names of the proteins
  3. Naming Convention: type of the UniProt accession (Swiss-Prot or TrEmbl)
  4. Major Loc With Loc Score: list of the major cellular components and the relevant Localization Scores
  5. Minor Loc: list of the GO terms of the minor cellular components
  6. Loc Experimental System Type: contains the system type of the localization data: experimental, predicted, or unknown with more detailed name if it was available
  7. Loc Source DB: list of the source databases of the given localization entry
  8. Interaction Source DB: list of the source databases for the given interaction
  9. Taxonomy ID: the taxonomy ID of the given protein

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ComPPI is published in Nucleic Acids Research Database Issue 2015