Wednesday, November 1, 2017

Visualising sub-cellular locations in UniProt

The UniProt Knowledgebase provides protein entries covering key aspects of protein biology divided into sections that group related information.

One of the sections on the protein entry pages is Subcellular Location. This section provides information on the location and the topology of the mature protein in the cell. You can now visually explore the subcellular location in UniProtKB entries. The visualisation presents image templates from COMPARTMENTS combined with protein location data from UniProt (expert annotation, rule-based automatic annotation) and imported from Gene Ontology (GO) annotation. The figure below shows the subcellular location view from the Human Copper-transporting ATPase 2 protein.

Colour-coded by evidence

The subcellular locations in which the protein is found are shown using colours and titles for the compartments. The colours can be gold which indicates 'Manual annotation' and blue which indicates 'Automatic computational assertion'. These colours are also reflected in the clickable evidence tags on the right hand side in the tabs showing the text annotation.

Source-based annotation tabs

There are two tabs based on the sources of annotation, one for UniProt annotation and one for GO (Gene Ontology) annotation. You can click on the tabs to view the specific annotation from that source. The image on the left hand side will update to reflect the annotation tab that you are on.

Click to highlight

You can also click on a coloured subcellular location compartment to quickly highlight the corresponding annotation on the right hand side. 

Try it out and let us know what you think! What else would you like to see visually in the UniProtKB entry?

No comments:

Post a Comment