CCLE_mutations data mismatch

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1

The list of mutations for HOXC6 from the “CCLE_mutations.csv” file (22Q2):

|Silent|25|
|Missense_Mutation|19|
|Nonsense_Mutation|2|
|Frame_Shift_Ins|2|
|Frame_Shift_Del|1|

This data does not match with the graph on the DepMap website.

Best,
Saed

2

Hello,

Thanks you for raising this issue. On first glance I think I see what you mean but I can’t think of any explanation for it. The number of Silent mutations is greater than what the histogram shows. I’m logging this as a bug for a developer to investigate.

Thank you,
Phil

3

This was so puzzling, I took a quick look and now I understand what’s going on.

The histogram is counting the number of cell lines for each variant, not actually the literal number of mutations. That is to say, if cell line X has 2 “Silent” mutations in gene Z, and cell line Y has 1 Silent mutation in gene Z, it would count that as “2 cell lines have silent mutations in gene Z”

This is reflected in the label on the x-axis which says “# of cell lines” and I had missed the first time I took a look at the plot.

As a result, I believe this is working as designed. (Although it’s debatable whether # of cell lines makes more sense to count, or # of mutations)

Thanks,
Phil

4

Thank you, Phil.
Saed