Results for quantitative input data

If you submit data in a format that includes columns of numeric values, following a first column of protein, compound or other suitable identifiers such as probe IDs, the analysis tool will interpret your data as expression data. The numeric values are used to colour objects in pathway diagrams. This view was created for microarray data, but any dataset that consists of a list of identifiers with associated numeric values can be used, e.g. quantitative proteomics, GWAS scores.

The results page is very similar to that of a qualitative input analysis (single-column list of identifiers) with additional columns in the Analysis details (Figure 17). These extra columns represent the submitted expression values (red box in Figure 17). Clicking on a pathway name launches the relevant pathway diagram.

Things to look for:

• Objects in the Pathway diagram are coloured according to the numeric values submitted. The gradient yellow to blue colours are based on a scale, which is represented in a bar on the right hand side. 
• When zoomed out, objects are coloured to reflect the average of the values submitted for the molecules. When zoomed in, complexes and sets will resolve to coloured bands, representing the values of individual molecules. 
• To view details of the components of a complex or set, hover the mouse pointer over it and a small blue triangle will appear on the right side. Select this to open the information panel that has details on relevant molecules, pathways and interactions.
• The experiment browser toolbar (grey panel at the bottom) is used to step through the columns of your data, e.g. time-points or disease progression. As you move across the different columns, the pathway diagrams will re-colour to reflect the new values.