Thursday, November 9, 2017

Visualising protein interactions in UniProt

The UniProtKB entries include an Interaction section, which details the protein’s binary interactions with other proteins, using a high-quality dataset supplied by the IMEx Consortium.

You can now view the binary interactions in a graph that shows the interaction partners of your protein and also shows which of those partners interact with each other. For example, here is the interaction matrix for the human E3 ubiquitin-protein ligase parkin protein.

Dots dots dots

Each interaction edge is represented by a dot, of which the intensity represents the number of experiments supporting the interaction. Hovering over the dot highlights both partners.

Information on click

Clicking on an interaction dot brings up a popup window with details about the interaction.

This window contains more information about the interacting partners:

  • Names
  • Identifiers and link to UniProt entry
  • List of diseases, and link to the relevant section of the UniProt entry
  • Subcellular location
  • Number of experiments, and link to IntAct

Filtering the display

We currently have two filters which allow users to filter out data from the graph. They apply if any of the partners in the interaction satisfy the selected criteria.

The two filters are:

  • Subcellular location: this is a tree-based selection menu which allows users to filter proteins based on their location within the cell
  • Disease: only show proteins which are involved in the specified disease(s)
We are working on enhancing this view further. Are there any more filters or other improvements that you would like to suggest? Let us know!

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