drug_sensitivity: drug_sensitivity_21Q2

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

drug_sensitivity_21Q2

Description

The 'drug_sensitivity' dataset contains the 19Q3 replicate collapsed logfold change values relative to DMSO, corrected for experimental confounders using ComBat. This dataset contains information refering to 4686 compounds, 578 cell lines, 23 primary diseases and 25 lineages. This dataset is part of the SIGMA Re-purposing release which contains small molecule viability datasets generated using the Broad Re-purposing Library and the PRISM multiplexed cell-line viability assay. The columns of 'drug_sensitivity' are: 'depmap_id' a foreign key corresponding to the cancer cell lineage, 'cell_line' the common CCLE name of the cancer cell lines, 'compound' the synonym for the drug compound, and 'dependency' which contains the numerical dependency score values for each pair of genes and cell lines. Compounded metadata has also been added.

Usage

drug_sensitivity

Format

A data frame with 2708508 rows (cell lines) and 14 variables:

depmap_id

Cell line foreign key (i.e. "ACH-000956")

cell_line

Name of cancer cell line (i.e. "22RV1_PROSTATE")

compound

Drug compound name (i.e. BRD-A00077618-236-07-6::2.5::HTS)

dependency

numerical depenency score of a compound on a cell line

broad_id

Broad ID for compound (i.e. BRD-A00077618-236-07-6)

name

Standard chemical name (i.e. 8-bromo-cGMP)

dose

Dose of compound

screen_id

Broad ID for compound (i.e. HTS)

moa

Mechanism of action (i.e. PKA activator)

target

Molecular target of compount (i.e. PRKG1)

disease_area

Anatomical target (i.e. hematologic malignancy)

indication

Prescribed for disease (i.e. acute myeloid leukemia (AML))

smiles

Simplified molecular-input line-entry specification

phase

Clincal phase

Details

This data originates from the 'primary_replicate_collapsed_logfold_change.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. Note: compound metadata was added to this dataset, consisting of 10 new features derived from the file 'primary-screen-replicate-collapsed-treatment-info.csv' from the [Broad Institute](https://depmap.org/portal/download/) website. The Drug sensitivity data remains from 19Q3, however the version was bumped to 21Q2 to distinguish between the different datasets.

Change log

- 19Q3: Initial dataset consisted of a data frame with 2708508 rows (cell lines) and 6 variables representing 686 compounds, 578 cell lines, 23 primary diseases and 25 lineages.

- 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: Drug sensitivity data combined with compound metadata, added 10 new features from the file primary-screen-replicate-collapsed-treatment-info.csv

- 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.

Steven M Corsello, Rohith T Nagari, Ryan D Spangler, Jordan Rossen, Mustafa Kocak, Jordan G Bryan, Ranad Humeidi, David Peck, Xiaoyun Wu, Andrew A Tang, Vickie MWang, Samantha A Bender, Evan Lemire, Rajiv Narayan, Philip Montgomery, Uri Ben-David, Yejia Chen, Matthew G Rees, Nicholas J Lyons, James M McFarland, Bang TWong, Li Wang, Nancy Dumont, Patrick J O'Hearn, Eric Stefan, John G Doench, HeidiGreulich, Matthew Meyerson, Francisca Vazquez, Aravind Subramanian, Jennifer A Roth, Joshua A Bittker, Jesse S Boehm, Christopher C Mader, Aviad Tsherniak, Todd R Golub. 2019. Non-oncology drugs are a source of previously unappreciated anti-cancer activity. bioRXiv. https://www.biorxiv.org/content/10.1101/730119v1

UCLouvain-CBIO/depmap documentation built on March 24, 2024, 2 p.m.