mRNA expression (RNAseq) scatter plot issues

Hi, last week I had begun compiling data on mRNA expression in my cell lines fro specific genes, but this tool is no longer available? Is this a bug or is the tool for making a scatter plot no longer available?

when you say “scatter plot”, do you mean the Data Explorer tool?

That certainly should still be there. And we haven’t done anything to remove mRNA expression data.

On Wednesday we made an update which we rolled back an hour later, but that’s been the only change in the portal recently. I see you asked about this 3 days ago, so I don’t think it could be related to that.

Can you take a screenshot of where something is missing which you used to be able to see?


I think I am having a similar problem.
I was using a tool that compared mRNA expression on every cell line.
It looked like this:

Ah, I think I have a guess of what the issue is now.

The figure you included looks like one that the CCLE portal was generating and now you’re seeing the DepMap portal which doesn’t have the same plot.

(Updates to the CCLE portal stopped sometime in 2018 and recently we started redirecting traffic from the old CCLE portal to the DepMap site because it contains the original CCLE lines as well as additional characterization data has been generated in the last several years.)

One can generate a similar plot by looking at the characterization tab. (The primary difference is that the classifications are along the y-axis as opposed to the x-axis.)

Also, we’ve been using tissue lineage as opposed to disease for the categorization. You can request to see the breakout by disease by generating a plot in the Data Explorer tool by clicking “Explored relationships with other data” in the top right, and then telling it to group by primary disease under “view options”

Let me know if this addresses your needs or whether you’re still having problems with generating such a plot.


OK, that works!

Hi, I am in a similar situation to merfuer, trying to reproduce previous gene expression analysis using the new version. Is it possible to order the indications from highest to lowest expression using the new version?

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@pmontgom : I actually have the same question; is there a way to order the indications from high to low as I believe the previously used tool in the CCLE portal did this automatically. Thank you in advance!

Apologies, I missed duncang’s question earlier. Unfortunately, the plot doesn’t have an option to sort as it stands today. I can see there’s interest in this, so I’ll add it to the development queue.

@pmontgom I want to know the y axis’s value of every mutation cluster in the picture? Thankyou very much.

The y-axis of the plot is just the different categories (non-conserving, other, etc)

However, are you asking what does the y-axis represent within a category (that is to say, within a violin plot)?

If so, the answer is: the y value within a violin plot is randomly assigned. The points are “jittered” on the y-axis to avoid overplotting and allow you to see individual points. There is no meaning to the y-value within each violin.


Thank you for your reply very much !

Thank you for your reply.