mRNA coexpression of genes in various breast cancer cell lines

Q&A
1

HI,
I had used CCLE database before to correlate the mRNA expression of set of genes in various breast cancer cell lines. But now evrything looks changed. Earleir in CCLE I create d a dot plot using this link
https://portals.broadinstitute.org/ccle

image
But now with DepMap portal using Tools—Data Explorer. I can select Gene and type the gene of interest. But when I move forward for selecting datasets, I cannot select the mRNA expression in the tabs. Is it normal now? Or is there a different way to create a dot plot using mRNA expression data now.

Please let me know.

Regards
Apsana

2

In the portal, the mRNA expression data is simply labeled “Expression”. Generating the same plot as you’ve added your post:

image
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I see that the scale looks quite different, but I suspect that’s just due to the units being different between the two plots. I’m not sure what the units in your plot are, but based on the range, I suspect it’s something like log(RKPM), whereas the the units in plot from DepMap are log2(TPM+1).

(We do this because the log() creates points with extreme negative values, which in turn can drive correlations even when those those measurement are below the noise floor of the assay. To prevent undue influence from low values we add a pseudocount before taking the log in the newer datasets)

Thanks,
Phil