Species Comparison

The Species Comparison tool allows you to compare human pathways with other species to see what is common to both or perhaps missing in humans or in the model organism.

Species Selection

• Species comparison is launched using the ‘Analyse Data’ button in the Pathway browser header bar or the Analyze button at the top of the Pathway Browser.
• In the Species comparison section, select one of the species in the dropdown list. Click the ‘Go’ button (Figure 25).

Background operations

Reactome uses the manually curated human pathways to computationally infer their equivalents in other species. This inference process is based on gene orthology, using the Ensembl Compara database.

Biological processes are remarkably well-conserved over large evolutionary distances. Even though our focus is to annotate the molecular details of human biological events, we can use protein sequence orthology relationships to ask whether the human proteins involved in the reaction have orthologs in the model organism. If the orthologs exist in the Ensembl Compara resource, we computationally infer the corresponding reaction for the model organism and in this way build up a predicted pathway knowledgebase for the organism.

Results

Clicking on pathway nodes displays the relevant pathway diagram (Figure 26).

The colour of reaction objects indicates the result of the comparison:

• Yellow indicates that the protein has an inferred equivalent in the comparison species
• Blue indicates that no equivalent was identified. This protein may not exist in the comparison species
• No colour indicates that inference was not possible. This is always the case for small molecules, DNA and other objects that have no UniProt entry
• Objects with bands of colour represent complexes or sets containing more than one molecule. The bands of colour reflect the inference success for the molecules within the complex/set
• The species comparison bar at the bottom of the Pathway diagram (Figure 26) can be used to turn off Species comparison colouring.

To see the Species comparison results for the components of a complex (boxes with bands of colour), hover your mouse over the object and open the information panel (small blue triangle on right) (Figure 27).

To learn more about the pathway diagrams have a look at Understanding Pathway diagrams in our companion course Reactome: Exploring biological pathways.