Submission process

Selecting the Continue button on the Analysis submission form brings you to an options page (Figure 10). 

Several popular proteomics tools generate results that contain a mixture of human and other species identifiers. When the default option of Project to human is selected, all non-human identifiers in your query are converted to their human orthologous equivalents. As Reactome pathways represent human events, this conversion will maximise the chances of a successful match to a Reactome pathway. However, you may want to uncheck this box if your query represents data from an infected tissue, i.e. it consists of a mixture of human and microbial identifiers. To prevent conversion of non-human identifiers to human, uncheck the box.

For a graphical explanation of this option, click on the plus button underneath the header ‘Project to human’.

Include Interactors is unchecked by default. With this option selected, Reactome pathways are expanded by including all protein-protein interactors from the IntAct database for every protein represented by the pathway. This can greatly increase the size of the pathway and extend it to include proteins that would not otherwise be represented, which maximises the chances of matching your submitted identifiers to the resulting expanded pathways. However, the risk of this pathway expansion is that the expanded protein set has not been verified by manual curation and review. You should understand that IntAct interactions may be ‘false positives’, i.e. artefacts resulting from the technology used with no biological relevance.

For a graphical explanation of this option, click on the plus button underneath the header ‘Include interactors’.