Question: How to compare the gene expression signature of treated cancer cell and normal cell
0
gravatar for liuyang
4.3 years ago by
liuyang20
China
liuyang20 wrote:

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.

gene expression signature • 2.9k views
ADD COMMENTlink modified 4.3 years ago by Jie Ping20 • written 4.3 years ago by liuyang20
0
gravatar for Jie Ping
4.3 years ago by
Jie Ping20
China
Jie Ping20 wrote:

Did not understand your question exactly.

Spearman rank analysis is for qualitative data.

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

ADD COMMENTlink written 4.3 years ago by Jie Ping20

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?

ADD REPLYlink written 4.3 years ago by liuyang20
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2511 users visited in the last hour