Question: How to determine post-treatment expression from pre-treatment and differential expression?
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gravatar for avinashd.sahu
14 months ago by
avinashd.sahu0 wrote:

In most cell line experiments, it is widespread to perform RNA-seq for many cell-lines before or after a treatment (of a drug). Then, typically, differential expression analysis is conducted.

Now if I have a pre-treatment expression of a new cell-line, how to determine what will be its likely (the drug) post-treatment expression? Assume drug efficacy and response are the same across all cell lines.

rna-seq • 288 views
ADD COMMENTlink modified 9 months ago by Biostar ♦♦ 20 • written 14 months ago by avinashd.sahu0
1
gravatar for Kevin Blighe
14 months ago by
Kevin Blighe67k
Republic of Ireland
Kevin Blighe67k wrote:

You would have to build some form of a predictive / regression model using reference datasets consisting of pre- and post-treatment cell-lines, and then apply this model to the new cell-line in order to infer response (within a certain window of statistical error). How you define 'response' is your role, or that of the clinicians / biologists working with you.

Otherwise, if you know your drug and its target(s) quite well, then you may simply have to examine the expression of key target genes in your sample. For example, Trastuzumab (Herceptin®) targets ERBB2 / HER2; so, the cell-line would have to express this in order to respond to the drug. By simply examining normalised counts or Z-transformed expression data, one could infer heightened expression of a particular gene or genes.

Kevin

ADD COMMENTlink modified 14 months ago • written 14 months ago by Kevin Blighe67k

Any reference/paper that might have used such an approach?

ADD REPLYlink written 14 months ago by avinashd.sahu0
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