Question: Pathway analysis with co-variates for RNA-seq data
0
gravatar for JJ
7 months ago by
JJ470
JJ470 wrote:

Hi all,

I was wondering if someone knows of a tool to perform a pathway analysis with co-variates for RNA-seq data.

What I mean in more detail is the following: I have two groups (cond. 1 vs. cond. 2) but I also have co-variates which will have an high impact on the expression (20-30 samples in total, balanced design). Hence I am not sure that a standard DE analysis e.g. with voom/limma with co-variates will lead to significant results. I more expect that the same pathways will be up or down regulated than particular genes. Hence, I am looking for a gene-set based analysis where I can also give co-variates as parameters.

Thanks for your help!

rna-seq • 278 views
ADD COMMENTlink modified 7 months ago by Kevin Blighe49k • written 7 months ago by JJ470
4
gravatar for Kevin Blighe
7 months ago by
Kevin Blighe49k
Kevin Blighe49k wrote:

With GSVA, you can enrich your dataset against MSigDB, KEGG, Reactome, and Biocarta in an unbiased fashion and then perform a differential pathway / signature analysis while adjusting for covariates (usually via limma). GSVA will essentially return to you your same dataset with your genes replaced by pathways and their respective levels of activation.

I would highly recommend getting to grips with the program as it is very powerful for a diverse range of analyses. To give you an idea of things for which I have used GSVA:

  • simple pathway / signature enrichment
  • differential pathway / signature analysis while adjusting for covariates
  • disease predictive modeling using pathways, not genes
  • inferring scRNA-seq cell-types in bulk data (akin to cellular deconvolution)

Kevin

ADD COMMENTlink modified 7 months ago • written 7 months ago by Kevin Blighe49k

thanks so much for this pointer!

ADD REPLYlink written 7 months ago by JJ470
1

If you need help with code, then give me a shout.

ADD REPLYlink written 7 months ago by Kevin Blighe49k

will do - thanks so much!

ADD REPLYlink written 7 months ago by JJ470
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1976 users visited in the last hour