How to compare the gene expression signature of treated cancer cell and normal cell

Question

[liuyang]

I have the gene expression signatures of cancer cell lines and cancer cell lines treated with certain drug. Now I want to analysis if the gene expression of cancer cell treated with the drug is similar with the gene expression of normal cell lines. So I collected the gene expression signatures of normal cell lines from GEO. I noticed the data distribution of these two signatures (consists of 20000+ genes) are different, normalization is needed. Which method should I use to compare these two signatures? A simple Spearman rank analysis or GSEA? But GSEA is used to analyze differentially expressed genes, I can’t figure it out which gene expression signature should I compare with.

Answer 1

[Jie Ping]

Did not understand your question exactly.

Spearman rank analysis is for qualitative data.

Gene expression is quantitative data ,why not take a t-test?

[liuyang]

Sorry for ambiguity, I noticed that I should not compare the profile of normal cell with that of cancer cell line treated with drug directly since this does not make sense.

Now I want to collect the differentially expressed genes in the cancer cell lines(PC3, MCF7, etc.). So I need the gene expression signatures of normal cell and cancer cell. But I noticed that in GEO such data is very little. What's more, many samples does not have technical replicates. Do you have any idea that where can I find such data?