Skip to contents

K562 shRNA essentiality screen: reference essential and non-essential genes

Source: R/k562_data.R
k562_reference_genes.Rd

The core essential genes (CEGv2) and the non-essential genes (NEGv1) defined by Hart et al. from many genome-wide screens, restricted to the genes of k562_count_table. They are the standard reference to evaluate essentiality screens: the core essential genes should be depleted and the non-essential genes not.

Usage

data(k562_reference_genes)

Format

A data frame with 1585 rows (genes) and 3 columns:

Gene

The gene symbol.

Gene_ID

The NCBI (Entrez) gene ID.

Class

"core essential" (681 genes) or "non-essential" (904 genes).

Source

Hart T, Brown KR, Sircoulomb F, Rottapel R, Moffat J (2014). Measuring error rates in genomic perturbation screens: gold standards for human functional genomics. Mol Syst Biol 10:733. doi:10.15252/msb.20145216 . Hart T, Tong AHY, Chan K, Van Leeuwen J, Seetharaman A, Aregger M, et al. (2017). Evaluation and design of genome-wide CRISPR/SpCas9 knockout screens. G3 7:2719-2727. doi:10.1534/g3.117.041277

Details

The lists come from the BAGEL repository (https://github.com/hart-lab/bagel), distributed under the MIT license, Copyright (c) 2020 Hart Lab.

See also

k562_count_table

Examples

data(k562_reference_genes)
table(k562_reference_genes$Class)
#> 
#> core essential  non-essential 
#>            681            904