RPPA: RPPA_19Q3

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

RPPA_19Q3

Description

The 'RPPA' dataset contains the 19Q3 CCLE Reverse Phase Protein Array (RPPA) cellular model expression data. This dataset includes data from 214 genes, 899 cancer cell lines, 28 primary diseases and 28 lineages. The columns of 'RPPA' are: 'depmap_id', a foreign key corresponding to the cancer cell lineage, 'cell_line' which contains the common CCLE name of the cancer cell lines, 'gene' which contains the knockdown gene expression, 'antibody' containing the name of knocked down gene and 'expression' containing numerical protein expression data. This dataset can be loaded into R environment with the 'depmap_RPPA' function.

Usage

RPPA

Format

A data frame with 192386 rows and 4 variables:

depmap_id

cancer cell line foreign key (i.e. "ACH-000001")

cell_line

CCLE name of cancer cell line (i.e. "NIHOVCAR3_OVARY")

antibody

Name of antibody targeting protein (i.e. "14-3-3_beta")

expression

Observed expression via RPPA of protein coding genes

Details

This data represents the 'CCLE_RPPA_20181003.csv' file taken from the 19Q3 [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 192386 rows and 4 variables representing 214 genes, 899 cancer cell lines, 28 primary diseases and 28 lineages.

- 19Q2: no change

- 19Q3: no change, no further releases are scheduled at this time.

- 19Q4: no change, no further releases are scheduled at this time.

- 20Q1: no change, no further releases are scheduled at this time.

- 20Q2: no change, no further releases are scheduled at this time.

- 20Q3: no change, no further releases are scheduled at this time.

- 20Q4: no change, no further releases are scheduled at this time.

- 21Q1: no change, no further releases are scheduled at this time.

- 21Q2: no change, no further releases are scheduled at this time.

- 21Q3: no change, no further releases are scheduled at this time.

- 21Q4: no change, no further releases are scheduled at this time.

- 22Q1: no change, no further releases are scheduled at this time.

- 22Q2: no change, no further releases are scheduled at this time.

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.

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).

Haoxin Li, Shaoyang Ning, Mahmoud Ghandi, Gregory V. Kryukov, Shuba Gopal, ... Levi A. Garraway & William R. Sellers. The landscape of cancer cell line metabolism. Nature Medicine 25, 850-860 (2019).

Examples

## Not run: 
depmap_RPPA()

## End(Not run)

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