Skip to contents

Reference essential and non-essential human genes

Source: R/reference_data.R
hart_reference_genes.Rd

The core essential genes (CEGv2, 684 genes) and the non-essential genes (NEGv1, 926 genes) defined by Hart et al. from many genome-wide CRISPR and shRNA screens. They are the standard reference to check the quality of proliferation (dropout) screens in human cells with compute_screen_quality and to scale fold changes with scale_by_reference: the essential genes should be depleted and the non-essential genes not. k562_reference_genes is the subset of these genes present in the K562 dataset.

Usage

data(hart_reference_genes)

Format

A data frame with 1610 rows (genes) and 4 columns:

Gene

The gene symbol.

HGNC_ID

The HGNC identifier.

Entrez_ID

The NCBI (Entrez) gene ID.

Class

"core essential" or "non-essential".

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, 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 BAGEL2 repository (https://github.com/hart-lab/bagel), distributed under the MIT license, Copyright (c) 2020 Hart Lab. The script that builds the dataset is in the scripts folder of the installed package (system.file("scripts", package = "ScreenR")).

See also

compute_screen_quality, scale_by_reference, k562_reference_genes

Examples

data(hart_reference_genes)
table(hart_reference_genes$Class)
#> 
#> core essential  non-essential 
#>            684            926