Hi everyone, I am trying to find differentially expressed genes between 2 different breast cancer tumor models. One of the dataset is from RNA-seq while the other one is from microarray. I've been searching for a good way to do this but I haven't found anything that works. Can anyone who actually has done this please provide some advice?
Thank you!!!
3 answers
For microarray probe design, specific genes are targeted , which is not in the case of NGS dataset. That being said, you will never be able to find novel transcripts using microarrays. Also, the technical as well as wetlab aspects vary considerably in both the cases. Hence, the best way, as suggested by Sparrow_kop is to evaluate overlapping DE genes.
Hi Vijay, In iPathwayGuide, we have a feature that allows you to conduct a Meta-Analysis to identify overlapping DEGs across up to 5 separate datasets. The application is agnostic to the platform use to measure expression. I have customers that routinely compare mRNA to protein expression or RNA-Seq based expression to microarray. Not only will you see overlapping genes, but you can also identify common or uniqly perturbed pathways and the set of genes that are driving that change.
Unfortunately, this feature is a premium feature and normally requires payment. If you reach out to me and mention this post, I'd be happy to arrange a way for you to get some free reports. You can reach me by email: andrew "AT" advaitabio.com I've pasted a few images below. to give you a sense of what it can do for you.
may be useful, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3617154/
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In my opinion, I think there are technology bias and bench effect to the two different kind of dataset. So maybe you could find DE gene in the two dataset separately, and then evaluate the overlapping DE genes.