Need some help with next steps after getting fGSEA results from Microarray data.

Question

[biotrekker]

Hello all! I am relatively new to bioinformatics. I am currently a PhD student who works on the data science side of bioinformatics. I currently work with Microarray and RNAseq data but plan on working with other NGS data. I want to be good at what I do and understand the decision making process behind a lot pipelines and analytics.

At the moment I am working on differential expression data analysis (of Microarray data) with fGSEA. I understand that I have enriched ontologies and leading edge genes that are responsible for said enrichments. What I don't understand is what I have to do next. I'm new to writing papers so I don't know what to do. What do I do next to have publishable results.

I understand my question(s) are a bit vague and generic but any help is appreciated!

Thanks!

Answer 1

[charlielonergan]

I'm using fgsea currently and have a similar task. I recently found clusterProfiler (http://yulab-smu.top/clusterProfiler-book/chapter12.html) to be a useful package for visualising the results of your GSEA, and wish I had found it 2 months ago.

You can visualise the top genes/pathways in a network, for example. Then generally you're going to do a lot of googling of those genes/pathways in how they relate to your biological question.