# Nomenclature of essential genes

**URL:** <https://forum.depmap.org/t/nomenclature-of-essential-genes/567>\
**Category:** Q&A\
**Created:** [April 21, 2021, 2:52pm UTC](https://forum.depmap.org/t/nomenclature-of-essential-genes/567 "2021-04-21T14:52:57Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![abct](https://avatars.discourse-cdn.com/v4/letter/a/94ad74/32.png) [@abct](https://forum.depmap.org/u/abct)\
**Post date:** [April 21, 2021, 2:52pm UTC](https://forum.depmap.org/t/nomenclature-of-essential-genes/567/1 "2021-04-21T14:52:57Z")

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I tried to understand “genes essentiality” classification and the best way to identify them.

Genes (within a cell line) with probability of dependency \> 0.5 are classified as **essential** for the cell line and the other **non essential**.  
For each genes, based on all cell lines values for dependency score, one performs a normality likelihood test test. If a gene has a normLRT score \> 100 (ie it is closer to a Student distribution than a Gaussian one, ie there are outliers), it is called a **selective dependency** (independently of the cell line).  
Within a cell line, an essential gene is call **strongly selective** if it’s a selective dependency and **common essential** otherwise.  
Am I right?

In the Tsherniak paper (2017), (I understand that) they try to identify an equivalent of the strongly selective class, the **differential dependency** class, by selecting cell line - genes dependency effects that are smaller that mu - 6 \* sigma (where mu and sigma are the mean and the standard deviation of the dependency effects among all cell lines for the considered gene).  
What do you recommend to use to identify these interesting genes among a cell line? Probability \> 0.5 and normLRT \> 100, or deviation from the mean \> 6 \* sigma?

Thanks a lot!

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**Author:** ![Joshua\_Dempster](https://yyz1.discourse-cdn.com/flex035/user_avatar/forum.depmap.org/joshua_dempster/32/19_2.png) [@Joshua\_Dempster](https://forum.depmap.org/u/Joshua_Dempster)\
**Post date:** [April 21, 2021, 8:12pm UTC](https://forum.depmap.org/t/nomenclature-of-essential-genes/567/2 "2021-04-21T20:12:24Z")

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Hi,

I’m not familiar with a selective designation. Strongly selective means the gene’s profile has normLRT \> 100. Either method you suggest for identifying interesting dependencies within a cell line would work, although I would not generally suggest trying to identify interesting genes within a single cell line.

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**Author:** ![abct](https://avatars.discourse-cdn.com/v4/letter/a/94ad74/32.png) [@abct](https://forum.depmap.org/u/abct)\
**Post date:** [April 22, 2021, 9:33am UTC](https://forum.depmap.org/t/nomenclature-of-essential-genes/567/3 "2021-04-22T09:33:43Z")

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Thanks for your answer.

> [@Joshua\_Dempster](#):
>
> I would not generally suggest trying to identify interesting genes within a single cell line.

However I don’t understand what you mean here. It is not appropriate to say that gene X is essential for cell line Y if its probability of dependency P\_{X,Y} is greater than 0.5 (or another threshold)? Did I miss something?