From RNA seq to cell receptor targets.

Question

[TonyCN]

I understand that this is a very broad question, so please bear with. I'm hoping to fill in knowledge gaps so I can go away with the correct 'nouns' and learn for myself.

I have performed RNA seq analysis and GO analysis on data from a small drug screening on iPSC human stem cells. With the understanding of what is being up/do regulated when exposed to a drug, I would like to go backwards and identify the pathways and ultimately those receptors responsible for the expression profile. I would be grateful if anyone could share with me what those steps are?

Answer 1

[ATpoint]

Instead of using the very broad GO terms I suggest you use tools such as g:profiler2 to actually scan for enriched terms against the KEGG and REACTOME databases. REACTOME has a nice pathway explorer interface that you can then use to zoom-into pathways, exploring the involved genes. Be sure that when using g:profiler2 you use all genes from your RNA-seq as background. When you use edgeR then e.g. the genes that survived FilterByExpr or DESeq2 the genes having non NAs after the independent filtering. Backgrounds are crucial for proper enrichment results and to avoid unspecific enrichments simply by chance despite the internal statistics of the tool.

https://biit.cs.ut.ee/gprofiler/gost

https://reactome.org/PathwayBrowser/

[TonyCN]

Thanks! Very helpful and exactly what I needed to know get set me on the right path.