HOW TO PERFORM GSEA - A tutorial on gene set enrichment analysis for RNA-seq

In this tutorial, we explain what gene set enrichment analysis (GSEA) is and what it offers you. We show you how to run the analysis on your computer and take you through how to interpret the outputs. The tutorial also covers leading edge analysis and analysis of gene networks with Cytoscape.

The timestamps for the following sections are:

0:09 What is GSEA?
9:09 What software do I need?
9:55 What input files do I need to create?
14:12 What gene set files are available?
19:04 How do I use GSEA software?
35:57 What is leading edge analysis?
40:05 Visualising enriched gene sets as a network

GSEA website (download free software here)

GSEA User Guide

The Gene Set Database

Cytoscape network analysis software

This tutorial on GSEA is brought to you by Dr Katherine West in the College of Medical Veterinary and Life Sciences at the University of Glasgow, Scotland. Look out for our other videos in this tutorial series that will help you get the most out of your gene expression analysis.

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[oscaramadori]

Just leaving a comment hopefully for people that are trying to use it recently.
The Expression Dataset File by default is no longer like that: just remove the first 2 rows (starting with the row: Name "tab" Description "tab" ...)
I did that and everything run smoothly! You can also see it as the last example in the user guide web page
(did they change the default standard?)

[vigneshwaranvenkatesan]

I literally didnt like anlaysing the RNAseq data for my project samples for the past 1 year. After seeing your video, it was eye-opening.

[SNAKE]

It was about time that I was searching for a "real" GSEA tutorial. Thanks very much!

[acastanza]

This was really a really well done, in depth walkthrough of GSEA!

[nwislamicschool]

An excellent presentation and made GSEA understand quickly. I recommended this to my colleagues and co-researchers- Very well done.

[blackV]

I have a note about what you said at 3:33
The genes are ranked based on their P. Value and fold change, so saying based on counts isn't entirely true.
Thank you so much for the video it's really helpful.

[mohsennafshar]

Thank you for this helpful tutorial! I like how you explained all the output metrics in detail. I had zero encounters with RNA seq data analysis and within a few hours, I managed to compare my gene sets of interest in my experimental groups.

[VincentZhao-pbhs]

such a enjoyment to listening this clear explanation with such clear English speaking

[CYRG]

Thank you so much for the detailed tutorial. Its alot easier to understand than the user guide which misses out details on the input and ranking.

[fgfanta]

3:20 my understanding from reading the paper is that the genes ranking is based on some measure of correlation between the gene expression and the phenotype class, not just the average of the expressions for that gene. I don't think they are the same.

[mohammedimrankhan]

The tutorial was amazing and easy to follow. Well done and looking forward to future videos.

[MenglinJiang]

what a wonderful course! I do watched several before this one, this is the best!!!

[allisonk.miller]

Thank you! This was a great introduction to GSEA. I found it extremely helpful. I wish they did more tutorial like this for other software!

[saeidehmaleki]

Thanks so much again for helping me with fixing my files. That was a huge support.

[TheKhemrajthakur]

Such a wonderful and informative Illustration of GSEA. Thank you so much.

[kgbly]

Hi Dr. West, great tutorial. I have one question looking for your help. When creating Phenotype labels file in excel, you mentioned to save as tab-delimited text file with the extension.cls. How to do this? Excel does not have an option to save a file as cls file. Thanks.

[yaseenkattan]

Mandatory viewing for using the tool, thank you!

[analiasoledad]

This video is amazing, so far my favorite. Really clear and straightforward, I truly appreciate it! Great job! many thanks :)

[xuzhiwen]

Super helpful and clear tutorial! I appreciate you saved me a lot time to figure out how to do such analysis!

[wiggiag]

Thank you but how did you make the Venn Diagram?