Should I take the mean value for cell-line data?


Since there are cell line datasets (mutation, gene copy number etc.) for each quarter of each year, should I treat the different quarters as separate readings for the same cell line or remove repeated cell lines in different quarters and years?

Thank you,

Hi, our data from quarter to quarter is cumulative, meaning that unless there has been some issue or changes to pipelines, etc, we make sure the data is only being added as new cell lines. So you can just use the latest version of our data as the most up-to-date.

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I see, thank you! Is that why the latest versions (21Q4) have more cell lines than previous versions? I can see that the number of cell lines change in the sample info for each quarter and year.
I also wanted to ask, why some DepMap IDs do not have a corresponding COSMIC ID. Is there a way to find the missing COMIC IDs?

We loaded the mapping between COSMIC and DepMap IDs at point in the past and we don’t currently have a process to periodically update the mapping.

Some DepMap IDs might not have a corresponding COSMIC ID if they’re not in COSMIC’s collection, but it can also be the case that we don’t have the COSMIC ID because the line was added to our registration after the last time that we loaded the COSMIC ID → DepMap ID mappings.

We’re currently exploring how to better keep our registration system in sync with other resources, so you can expect that to improve in the future. However, in the mean time, if you want to check any lines, I’d recommend checking with Sanger’s Cell Line Passport or Cellosaurus because they also information about which lines correspond to different IDs and it’s possible that they have some COSMIC IDs that we’re missing.

On both sites you can look up a DepMap ID and get a page containing all the IDs associated with that line, which includes COSMIC.

For example: Cell Model Passports and Cellosaurus cell line CAL-72 (CVCL_1113)

We will eventually get our mapping updated as well, but I don’t have an estimate for when to expect that.