Gene Set Enrichment Analysis using RNA Sequencing Data 🧬

Pathway analysis is common for RNAseq downstream analysis. I will show you step by step How to do gene set over-representation analysis and gene set enrichment analysis. #rstats #bioinformatics #computationalbiology #lecture
Download the script at github.com/cra...

[@chrislee8408]

Thanks for this useful video! One question - I have, let's say 4 GSEA's to do for 4 DESeq2 results (4 different DESeq2 comparisons; 4 treatments compared to the same control), how can I visualize them "all together" in a dotplot or barplot to investigate the GO terms that they have in common/different? Thank you!

[@synatkeam5597]

Thank you Dr for very informative tutorial. I am wondering whether you could suggest how to do this with DEG output from Seurat? From seurat FindMarker Function, we get gene name, p_value, avg_log2FC, pct.1, pct.2 and p_val_adj. We do not have baseMean like DESEq2 at all. I tried to do it with my data, but was not succeed. Hope you could guide. I wanted to test enrichment using hallmark geneset. Thank in advance!

[@chatomics]

You can rank the genes with the p value and follow crazyhottommy.github.io/scRNA-seq-workshop-Fall-2019/scRNAseq_workshop_3.html

[@poonams4029]

Sir,
I don’t have knowledge of R programming or any other computer language.
But I want to GSEA analysis of my rna seq data. Can you suggest any methods

[@chatomics]

You can use www.genepattern.org/modules/docs/GSEA/14

[@poonams4029]

@@chatomics sir. I have used the link as provided by you. I have preranked DEGs file with log2FC and I have saved it in txt format as .rnk as mentioned in the module. But unfortunately got error. please provide insight into this

[@chatomics]

@@poonams4029 what errors did you get?

[@mahanishjungthapa6416]

Thanks for this video. I am a bioinformatics student. I have two queries.
1. After using enrichGO function we get the GO terms. But how to get the parent terms of certain specific level for a list of 100 GO terms ?
2. How to change the RNASeq RSEM values into TPM values ?

[@chatomics]

Not sure about 1. For 2, RSEM is TPM according to this post www.biostars.org/p/162170/

[@leeminho1193]

Thanks for useful video !

[@chatomics]

you are welcome!

[@abdc382]

I was trying to run over-representation analysis for the DESeq2 data that was compared between two cell lines for the ontology term cellular component in order to know what gene is enriched in which part of the cell. But, when I run enrichGO, it returns a data frame with zero rows.
There is no error message that is shown as well and hence I seem to be a little lost. Can you please let me know why that happens?
Thanks

[@chatomics]

That means no terms are enriched

[@piyalsaha3108]

That's an amazing lecture!

[@chatomics]

Glad it is helpful!! Spread the word :)

[@whqiao1722]

This video is exactly what I am looking for.

[@chatomics]

Great to hear!

[@santosh_333]

Much awaited 😊

[@chatomics]

let me know if it helps!