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  3. ChIP-seq with Bioconductor in R

Exercise

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.

Instructions

100 XP
  • 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.