How to know if certain gene is highly expressed compared to some common housekeeping gene in a cell line?

Question

[leranwangcs]

Hi,

If I have a list of cell line, and 12 genes, and I want to check the expression of those genes in those cell line, how to achieve this? I don't have any sequence data, probably may need to go to find public dataset for doing this. But I'm not sure where to start

Thanks!

[leranwangcs]

Hi, thanks so much for the reply @jared.andrews07 and fracarb8!

I tried both DepMap and TRON cell line database, and by searching based on cell line name (for example: Jurkat), I can get a list of genes that expressed in this cell line.

But I didn't find any of the genes that I'm interested in showed up in that list. Does that mean the genes are not expressed in this cell line?

I also found that result lists from these two websites are different. For Jurkat cell line:

DepMap:

TRON:

I'm a little confused about which one to follow or can I use both of them?

Thanks so much! Leran

[jared.andrews07]

You didn't post your genes, so who's to know? My guess is whatever identifier you're using is out of date (or vice versa on the sites), though that's easy enough to check for 12 genes.

Answer 1

[jared.andrews07]

DepMap has the Cancer Cell Line Encyclopedia data browsable, which has a ton of cell lines. May be worth starting there.

Answer 2

[fracarb8]

Have a look at the TRON cell line database. You can use the portal, or you can download the expression matrix and filter it yourself. In addition, TRON also provides other data, such as mutation, HLA alleles, viruses insertions. Another cell line resource is CCLE, and you might want to check both, as some cell lines can be found in one or the other.