crispr: crispr_22Q2

In UCLouvain-CBIO/depmap: Cancer Dependency Map Data Package

crispr_22Q2

Description

The 'crispr' dataset contains the 22Q2 genetic effect of CRISPR-Cas9 gene knockout of select genes in various cancer cell lines. This dataset includes data from 17386 genes, 1086 cell lines, 31 primary diseases and 28 lineages. The columns of 'crispr' are: 'depmap_id' a foreign key corresponding to the cancer cell lineage, 'cell_line' containing the common CCLE name of the cancer cell lines, 'gene' containing both the HUGO gene name of the knockout gene along with entrez ID#, 'gene_name' containing only the HUGO gene name, 'entrez_id' containing only the entrez ID# and 'dependency' which contains the numerical dependency score values for each pair of genes and cell lines. This dataset can be loaded into R environment with the 'depmap_crispr' function. NOTE: the 'crispr' dataset has replaced the 'rnai' dataset as the primary supported measurement of cancer dependency data as of the 19Q4 release.

Usage

crispr

Format

A data frame with 18881196 rows (cell lines) and 6 variables:

depmap_id

Cancer cell line foreign key (i.e. "ACH-00001")

gene

HUGO symbol (e.g. "SAP25") and Entrez ID# (e.g. 100316904)

gene_name

HUGO symbol (e.g. "SAP25")

entrez_id

Entrez ID# (e.g. 100316904)

dependency

numerical depenency score of given gene and cell line

cell_line

CCLE name of cancer cell line (i.e. "184A1_BREAST")

Details

This data represents the 'Achilles_gene_effect.csv' file taken from the 22Q2 [Broad Institute](https://depmap.org/portal/download/) cancer depenedency study. The derived dataset found in the 'depmap' package features the addition of a foreign key 'depmap_id' found in the first column of this dataset, which was added from the 'metadata' dataset. This dataset has been converted to a long format tibble. Variables names from the original dataset were converted to lower case, put in snake case, and abbreviated where feasible.

Change log

- 19Q1: Initial dataset consisted of a data frame with 9839772 rows (cell lines) and 6 variables representing 17634 genes, 558 cell lines, 26 primary diseases and 28 lineages.

- 19Q2: adds 5 cell lines, 1 primary disease and 1 lineage

- 19Q3: adds 699 genes, 62 cell lines and 1 primary disease. Now a dataset with 11458125 rows and 6 variables.

- 19Q4: adds 0 genes, 64 cell lines, 1 primary disease and 0 lineages.

- 20Q1: adds 50 cell lines.

- 20Q2: adds 30 cell lines.

- 20Q3: adds 20 cell lines, 1 primary disease and 1 lineages.

- 20Q4: adds 19 cell lines, 1 primary disease and 2 lineages

- 21Q1: no change

- 21Q2: removes 474 genes and adds 182 cell lines 1 primary disease and 1 lineage

- 21Q3: removes 252 genes and adds 42 cell lines

- 21Q4: removes 7 genes and 22 cell lines

- 22Q1: adds 16 cell lines and 1 lineage

- 22Q2: adds 16 cell lines and removes 1 primary diseases and 3 lineages.

Source

DepMap, Broad Institute: https://depmap.org/portal/download/

References

Tsherniak, A., Vazquez, F., Montgomery, P. G., Weir, B. A., Kryukov, G., Cowley, G. S., ... & Meyers, R. M. (2017). Defining a cancer dependency map. Cell, 170(3), 564-576.

DepMap, Broad (2019): DepMap Achilles 19Q1 Public. https://figshare.com/articles/DepMap_Achilles_19Q1_Public/7655150 Fileset.

Robin M. Meyers, Jordan G. Bryan, James M. McFarland, Barbara A. Weir, ... David E. Root, William C. Hahn, Aviad Tsherniak. Computational correction of copy number effect improves specificity of CRISPR-Cas9 essentiality screens in cancer cells. Nature Genetics 2017 October 49:1779–1784.

Mahmoud Ghandi, Franklin W. Huang, Judit Jané-Valbuena, Gregory V. Kryukov, ... Todd R. Golub, Levi A. Garraway & William R. Sellers. 2019. Next- generation characterization of the Cancer Cell Line Encyclopedia. Nature 569, 503–508 (2019).

Examples

## Not run: 
depmap_crispr()

## End(Not run)

UCLouvain-CBIO/depmap documentation built on Aug. 18, 2024, 9:46 p.m.