Copy number data

Hello! I am brand new to DepMap and enjoying it so far. I am interested in obtaining information about the copy numbers of various genes of interest in two cell lines. When performing a Custom Download, I noticed 2 options: “Copy Number Public 23Q2” and “Copy Number Absolute.” I was hoping you could either direct me where to look or provide me with more clarity about how these differ in terms of the origin of these numbers and how they are processed? Thank you!


Thanks for reaching out!

“Copy Number Public 23Q2” contains relative copy number data. If you navigate to the file downloads page and click on OmicsCNGene.csv, there is more explanation on how the data is computed.

On the other hand, “Copy Number Absolute” contains absolute copy number data generated using the ABSOLUTE algorithm. Essentially, the copy numbers are integers instead of ratios. I will note that this file was generated as part of the CCLE2 paper, and does not include any new depmap cell line data sequenced since then.

Hope this helps,

Hello, I am looking for the “Copy Number Public 23Q2” file but cannot find it. Is there also a dataset available that includes copy numbers for both chromosomes X and Y? The absolute_combined file does not have those. Thank you.

Hi @geart ,

If you are looking on the File Downloads page and select “DepMap Public 23Q2”, there should be a file called OmicsCNGene.csv which is the same as “Copy Number Public 23Q2” in the Custom Download page/data explorer.