The Pathway Analysis component can be used to find clusters of co-expressed genes sharing the same pathway. This can give you an idea about why they are co-expressed.
The data in this analysis component is read from a set of files that can be downloaded from the KEGG database either manually or automatically from J-Express. The kegg data files are proprietary and owned by KEGG. Note that you may have to obtain a license from KEGG to use the data before downloading. The J-Express license only allows you to use the J-Express framework fo facilitate the Kegg data, but does not grant you the rights to use the data.
Read more at Kegg
It is also important that you are able to map your data to Kegg data files. To do this, there must be some annotation in your data that can be linked to the data in the kegg files. To find more information about KEGG Identifiers, see the KEGG Identifiers page
Note: Kegg data is free for academic use.
Example of Pathway analysis
