Ideas For Presenting Pathway Enrichment

Question

[ChIP]

Hi!

I have performed Pathway Enrichment Analysis on 4 Sets of genes.

For Each set I get some commonly targetted pathways and some uniquely targetted pathways, of course their is a difference in their p-value and the number of genes enriched in commonly targetted pathways.

Now, this information can be represented in various ways, one of the commonly used methods is to create a table and put this information into it. But I am afraid tabular visualisations are not the best ways to represent results, specially while making presentations.

I am seeking ideas to represent my information on Pathway enrichment for 4 sets of genes, where I aim to highlight the commonly targetted pathways and the uniquely targetted pathways. What I could think of was of a heat map based on p-values or number of genes (I don't know if this will lead to good presentation of enrichment).

Any ideas and suggestions are welcomed and just in case if you think this will lead to another meta-analysis, feel free to put in your advice.

BTW the analysis was carried out using molecular signature database of GSEA (Broad institute).

Thank you

Answer 1

[k.nirmalraman]

I came across a nice visualization method in one of the R packages called ClusterProfiler.

May be this can be one of the ways, I would also be interested if there could be other methods!

[ChIP]

Hey thanks, I am trying to make this package work but it just doesn't. Have you used it? if yes then how can I proceed with my genelist for 3 sets. Thank you.

[k.nirmalraman]

Hi, Could you elaborate a little bit of your problem, I did customize a lot on the source code for my needs. But it was definitely possible to atleast reproduce the manual graphs!!

Also, I used GO db for enrichment and it required converting to the same format as that used in this package...