Pathway Analysis For Paired Microarray Data & Paired Rna-Seq Data?

Question

[michaelsbreen1]

Hi All,

I am pursuing Pathway Analysis for two different analyses. The first is a paired microarray dataset and the second is an RNA-Seq paired dataset.

Many tools available for pathway analysis don't take into consideration paired (matching) data. In the microarray world exist much methodology on how to rank a list of genes (for example WAD and FC methods) then feed this preranked into the tool, if it doesnt already have a tool built in to do the ranking. Is anyone aware of either

A. methodolgy to rank paired data across numerous subjects or B. tools that will incorporate paired data into the analysis.

I am aware GSEA, PathwayExpress, GeneTrail and David will not take matching data into consideration.

Additionally, I am interested to know if there are any pathway analysis tools apart from GO-Seq that is compatible with RNA-Seq data.

Best, Michael

Answer 1

[Heather Vincent]

I don't know of any program that will do exactly this, but you might consider using the difference between pairs as the input to an analysis. eg. If you are looking at expression before and after treatment, you might use after-before as the input.

Answer 2

[dompearcejankowski]

Hi Michael, did you ever reach a solution to your question? I'm in a similar boat right now though there doesn't seem to have been any progress in this regard in the last 23 months!

Much appreciated,

Dominic