A closer look at pathways
In this exercise, you will construct a URL that links to a pathway identified by the enrichment analysis and highlights the genes with ChIP-seq peaks. This allows you to get an overview of how the genes, or rather, the proteins they encode, interact with each other and other proteins. With some experience, this can quickly suggest potential mechanisms that might explain the differences between the groups in the study.
The general format of these URLs is: https://www.kegg.jp/pathway/pathway/<pathway_id>+<gene_id>+...+<gene_id>
You will construct the URL required to display the top pathway from the enrichment analysis, highlighting the genes associated with peaks. The objects top_path and genes you created earlier are available for you in the workspace.
This exercise is part of the course
ChIP-seq with Bioconductor in R
Exercise instructions
- Add the pathway ID to the URL.
- Collapse the IDs for genes in the pathway that were associated with peaks into a single string, separated by
'+'. - Add the gene selection string to the URL.
Hands-on interactive exercise
Have a go at this exercise by completing this sample code.
# This is the base URL for all KEGG pathways
base_url <- "https://www.kegg.jp/pathway/"
# Add pathway ID to URL
path_url <- paste0(base_url, ___)
# Collapse gene IDs into selection string
gene_select <- paste(___, collapse="+")
# Add gene IDs to URL
path_url <- paste(___, ___, sep="+")