Results for qualitative input data

For single-column input list of protein/small molecule identifiers, over-representation and pathway-topology analyses are performed. The results will resemble the example shown in Figure 11.

The names of the columns are explained when you hover over the column name on the Reactome webpage and also in this section of the Reactome User Guide.

Analysis results are shown in the Analysis tab, within the Details panel. All Reactome pathways are shown, in blocks of 20 pathways, ordered by ascending false discovery rate (FDR) value obtained from over-representation analysis. In addition, the number of molecules matched/total number of molecules and FDR values are added to the right side of pathway names in the Pathway hierarchy panel. Reactions that contain any of the matching molecules are boxed in orange. When you click on the name of a pathway in the Analysis tab, the Pathway hierarchy will expand to show it and its name will be highlighted in dark blue. If it has sub-pathways, you can use the plus buttons to the left of the pathway name to reveal sub-pathways and reactions.

Click on a pathway name to open the appropriate Pathway diagram.

Analysis results can be filtered for various factors, including pathway size, significance threshold (p-value) and species, using the funnel shaped filter icon on the top right corner of the Details panel (Figure 11). By default, all molecules (protein, small molecules, genes, transcripts) are used for over-representation analysis. Subtypes of molecule can be selected from a drop-down list in the filter option. Selecting these subsets will re-display results that consider only the selected molecular subtype. Another option in the filter allows users to ignore disease pathways for the analysis as it might skew the results in some cases.

Identifiers not found

The Analysis tab in the Details panel has three buttons on its left (Figure 11). By default the Results button is selected. Below this is the Not found button that indicates the number of submitted identifiers that were not successfully matched to molecules in Reactome. Click on the button to produce a list. 

If a significant portion of the identifiers could not be matched to pathways then:

• Ether the identifiers are not compatible to use with Reactome and you should replace them with something more suitable
• Or the identifiers represent molecules that are not found in our pathways, but might be connected to a known or unknown definable process

Diagram overlay

Analysis results are also reflected in the diagrams of pathways and reactions in the Diagram panel above the Details panel. This includes the overview diagrams, textbook-style diagrams and SBGN views.