How to get the differentially expressed genes in cancer cell lines

Question

[liuyang]

I'm wondering is there a way to calculate the differentially expressed genes in cancer cell lines(e.g.,MCF7)? The gene expression data (microarray or RNA-seq) for cancer cell lines can be found in many projects, but corresponding normal cell does not exist. Is it sound to use the corresponding normal tissue(e.g.,breast) gene expression for the calculation, such as the Illumina Body Map? Or is there any project to characterize the genome features of these cancer cell lines?

Answer 1

[Jautis]

Fairly obviously, the best method to get a sound comparison would be to generate the data yourselves and make the comparison there were you can control for design elements.

Short of that, using a tissue is problematic because of cell type heterogeneity although it may give you a basic idea of what effect you may expect. I would not make any biological claim comparing to breast tissue; you will need the exact cell type. However, you could use it to see if further analysis is justified.

I'm unsure what you're looking for in 'a project to characterize the genomic features of these cancer cell lines'. Can you be more specific?

[liuyang]

Actually I mean the irregularly up- and down- expressed genes in the cancer cell lines.I need these gene lists for following analysis. So you think it is not suitable to use normal tissue for the comparison?

[Jautis]

If you only need them to identify a list of candidate genes, I think that may work. If you wanted to say that those sites are definitively differentially-expressed in cancer cells, you'll need to have the cell types matched. Otherwise you'll introduce a lot of false positives due to cell type effects

[liuyang]

OK, thanks for your advice!