A while ago, I performed a DepMap analysis to find the mean gene effect on Meshenchymal models, as shown in the attached image. Currently, I’m trying to repeat the same query using different parameters, but I can’t find it anymore.
Could you tell me if this feature is still available and how to use it again?
Thanks
Based on the axes labels, it looks like you’ve generated a waterfall plot of mean gene effect for models in some context called “Mesenchymal”.
The only hard part about regenerating this plot is “Mesenchymal” is a “context” and those are user defined sets, so I can’t tell exactly how you defined that contextl. There are many ways that one could define a set of mesenchymal lines. We haven’t decided on one set that we feel comfortable releasing as an authoritative list, however, we do have an example of how one could define mesenchymal.
When you open data explorer, there’s this example:
After clicking on the link, it’ll open that plot with “Mesenchymal” temporarily defined, but from here you can click on “Save context”
It will with then open context manager so you can see how it’s defined and save it as one you can use elsewhere. (I think we’re thresholding some MSigDB signature to define this context, but it was largely intended as an example and it may not be the best way to define this group.)
Now that you have the context you want, you can generate the plot by selecting “waterfall” for “Plot Type” and under y-axis you want to plot “multiple” and you want to plot the mean of the “Mesenchymal” context
The only thing missing is the labeled genes.
I don’t know how you’ve determined which genes you want to select, but if it’s a manually defined list, you can define a context for the list and then say you want those genes selected by clicking this link on the page:
That’ll give you the option to define a new “gene context” and if you do so, you can paste in your list of genes:
save it and then click “select … genes”
Now the waterfall plot will have those genes labled
