Cancer-cell-line-specific essential genes

Question

[english.server]

Hi all!

Is there a cancer-type-specific database of essential genes? Specifically, I am looking for genes whose deletion would lead to loss of cancer cell lines (or loss of their growth ,....) in Glioblastoma Multiforme.

Thanks indeed.

Answer 1

[Kevin Blighe]

Hi, you will want the DepMap CERES crispR data:

• https://depmap.org/ceres/
• https://depmap.org/portal/download/

They profiled virtually all cell-lines from CCLE.

Note: a negative CERES score indicates that the gene in question is more 'essential' for that particular cell-line's viability:

"A negative CERES score indicates that a gene knockout results in a slower growth rate of a cell line, and a score lower than − 0.5 indicates a notable reduction"

sources:

• https://www.nature.com/articles/s41598-021-91713-2

• https://www.nature.com/articles/ng.3984

• How to interpret CERES gene scores for genome wide CRISPR-Cas9 knockout screens?

Kevin