Common essentials

Q&A
1

Hello,

When I search for a specific gene, it is listed as a common essential gene: CRISPR (DepMap 22Q2 Public, Chronos): 956/957 COMMON ESSENTIAL!

However, this gene is not listed in the common essential txt file.

How should I interpret this?

Thanks a lot!

2

I think the confusion is due to what the portal means by “common essential” and how the “common_essential.csv” file is defined.

On the portal “common essential” is defined by looking at the CRISPR data:
image
So, if a portal flags a gene as “common essential” it means that it looks essential in this particular dataset.

However, the “common_essential.csv” file is defined as:

image
image2108×306 42.4 KB

or, in other words, these are genes that Biomen and Hart have published as “common essential”. (We use these as our reference set used to scale gene effect, so we want these to be independently derived)

I hope that helps address the confusion.

Thanks,
Phil