Assessing how similar/ different of activated pathways between multiple groups of samples

Question

[cwwong13]

May I know are there is any bioinformatics package (or method) that can do a statistical test on two or multiple groups of pathway analysis.

I have 4 conditions:

1. Wild-type, control
2. Wild-type, treatment
3. knockout, control
4. knockout, treatment

I did RNAseq on these groups and did a pathway analysis on treatment vs control separately on wild-type and KO animals. I would like to know is there a way to quantitatively assess the difference between the activated (or inhibited) pathways between the wild-type and KO animals upon receiving the treatment?

Answer 1

[LauferVA]

I would start by reading:

1. GSEA (Subramaniam et al. 2005)
2. WGCNA (Langfelder et al. 2008)

User guides as well as explanation pages (sometimes written by the authors) are helpful as well:

1. https://www.gsea-msigdb.org/gsea/doc/GSEAUserGuideFrame.html
2. https://horvath.genetics.ucla.edu/html/CoexpressionNetwork/Rpackages/WGCNA/

If these do not address your question, please let me know!

[cwwong13]

Thanks for your suggestions, however, I am looking for a way to do differential gene analysis equivalent on pathways (should it call differential pathway analysis?). i know I should probably use DESeq2 od EdgeR for gene but not sure whether they will take pathway as input.

[LauferVA]

Right, that's why I included the WGCNA manuscript.