“Hi, I am currently using the web portal data explorer to investigate the gene effect of CCN4, but the results are puzzling me. Why do the outcomes of RNAi and CRISPR appear to be opposite? Of course, I have also noticed @pmontgom’s response regarding the data from RNAi screens and CRISPR screens, and I am aware that there are differences between these two datasets. However, this difference should not lead to an opposite gene effect for the CCN4 gene, right? This confusion is what I’m grappling with.”
My personal read of this comparison is less that the RNAi data is showing an opposite gene effect, but rather the two aren’t correlated. (When I saw the word “opposite” I was expecting to see correlation, but with an inverse relationship.)
Also, I notice the y axis has a very small range around zero (although centered a little above zero) so it looks like CRISPR is showing this gene to be non-essential in all of these lines, while RNAi shows some variance.
Looking at the global distribution, I see that are are very few lines that met the cut-off for us to call the line as “dependent”. (Only CRISPR had 3)
The scale of the variance is not that different then what I see when I look up a random olfactory receptor (OR10A2) which we expect to have no effect to viability:
There’s definitely a difference in the modes and means for this gene between the CRISPR and RNAi datasets (perhaps that’s what you meant by opposite?) but the scale of that difference is pretty small. I’m not sure how one can tell whether that difference is biologically meaningful or not.
