Creating a Data Set of Cell Lines That Have One Gene But Not Another

Q&A
1

Hi, I’m trying to download a data set of cell lines that express a certain X chromosome gene but NOT a certain Y chromosome gene. I was wondering if there was any way to do this through DepMap. Thanks for the help.

2

This seems like something I would do using “Cell line selector”

You can pull up a table with all lines and add a track for your X gene and a track for your Y gene:

(Just using two random genes (sox10, EGFR) in my screen shots)

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Once added, you’ve got those two columns:

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…and you can click the funnel to set which range of expression you’re interested in for the two genes being sure to click “exclude nulls” so we only are shown lines which have expression data.

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Now the resulting table shows only those lines with low SOX10 and high EGFR:

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and one can click the download icon on the bottom left to get a CSV of this table.

Hope that helps.

Thanks,
Phil