infering responsive genes from various experiments

Question

[zizigolu]

Hello,

I found 4 RNA-seq experiments about brasinosteroids in Arabidopsis, GSE52966, GSE35408, GSM912639 and GSE51772. but these experiment in addition to brassinosteroid, measured another hormones treatment like GA or IAA. My question is, is it reasonable to take samples focusing on brassinosteroids and ignoring another samples, then analysis these samples together to find something about BR responsive genes, network inference, so on?

Have a nice weekend

Answer 1

[andrew.j.skelton73]

Well, what do you want to find out about them specifically? - Generally speaking if you want to do an RNA seq experiment, you'd be carrying out a differential expression test at the gene or transcript level. What you're proposing (by the sounds of it), is to take a particular sample type (brasinosteroids in Arabidopsis) from three different sources..... then what? - You'd need to take the control samples from each of those experiments too.

In short, you're going to have a number of issues to deal with. The only saving grace of this, and that would make it potentially work, is that the samples in each experiment are the same, and prepped in relatively the same way too. If that's the case (you'll have to do some reading to make sure), then you could potentially use an additive model in DESeq2 for gene level differential expression analysis (~ Treatment + Effect). The reason you include a term for "Effect" is because there'll be huge amounts of variation between experiments, as such you need to control for this. You can only control for this effectively if you have samples of the same type within all levels of your "Effect" factor. This may not capture all the technical variation, but it's the best you can really do.

The alternative option is to treat each experiment independently, and treat each of them independently. This means that you can do the differential expression test for each GEO Accession, apply some filters and get a gene list, then look at the overlap between experiments.

[zizigolu]

andrew, really thank you for your explanation,

Samples within each GEO accession are not the same but each GEO accession has its own control against the BR treatment, for example in one experiment is BR treatment on root, in another experiment is on seedling,.., if I am going to infer a general BR effect of gene expression, can I take all samples together and count read for each gene and do differential expression alanysis for responsive genes?

[zizigolu]

Sorry andrew,

I got you 'samples in each experiment are the same...

Now, I have 4 groups from for experiments, each with two control and two treatments (2 replications), then here what could be my effect?

Thank you