Wednesday, 1 July 2015

Mapping a gene list onto KEGG pathways

In a previous post I discussed using GSEA to identify enriched KEGG pathways in my microarray data-set. After running the GSEA leading edge analysis I had a list of the genes that contributed most to the enrichment score for each pathway. I then wanted to examine where these genes fell within the KEGG pathway. The ‘user data mapping’ function in KEGG Mapper is a nice tool to achieve this quickly.

User data mapping

Select the ‘user data mapping’ option when viewing the reference KEGG pathway. In the pop-up window enter the gene symbols followed by the background and foreground color in hexadecimal numbers (if no color is specified the default is red).

Clicking ‘pathway mapping’ updates the reference to highlight the entered gene list. In this case it appears that my leading edge includes a sub-set of genes involved in methylation of histone lysine residues (in addition to the main pathway functions).

No comments:

Post a Comment