The bundled POWERUP example is a demonstration subset derived from DepMap Public 26Q1, available from the DepMap portal. It contains 300 selected reference cell lines, 300 selected expression features, four dependency responses, and two held-out expression profiles used as prediction samples. The subset was created simply for this POWERUP documentation and is not intended to reproduce the full DepMap release nor the results of any POWERUP publications.
Expression data
powerup_example_gene_expression.csv was derived from
DepMap Public 26Q1 table
OmicsExpressionTPMLogp1HumanProteinCodingGenes.csv, which
contains gene-level log-transformed TPM (Transcripts Per Million) values
from unstranded RNA-seq for human protein-coding genes.
The source table contains one row per profile, and the bundled POWERUP example retains 300 selected cell lines and 300 selected expression features, together with the sample identifier column only.
powerup_example_user_matrix.csv contains two expression
profiles held out from the 300 cell line reference subset. These
profiles use the same 300 expression features and serve as prediction
samples in the documentation examples.
Dependency responses
powerup_example_gene_dependency.csv was derived from
DepMap Public 26Q1 table
CRISPRGeneDependency.csv, which contains post-Chronos gene
dependency probability estimates for cell lines in the integrated
gene-effect data.
The bundled example retains the same 300 reference cell lines and four dependency responses: CTNNB1, ERBB2, FGFR1, and FAM50A.
Explanation models
powerup_example_explanation_models.rds is a compact
POWERUP object used by Explaining POWERUP
predictions. It contains CTNNB1, ERBB2, and FGFR1 models and retains
the training SHAP values and model metadata needed for explanation-path
analysis while omitting the original expression and response matrices,
fitted boosters, uncertainty models, and prediction data.
DepMap acknowledgement
The bundled example data are derived from DepMap Public 26Q1, provided by the Broad Institute’s DepMap program. The original DepMap release data are distributed under the Creative Commons Attribution 4.0 International (CC BY 4.0) license. The files distributed with POWERUP are modified subsets of the original release, containing selected samples, expression features, and dependency responses for documentation and demonstration purposes.
For the release used here:
DepMap, Broad (2026). DepMap Public 26Q1. Dataset. depmap.org
Manuscripts using these data should also include a reference to the DepMap portal.
The DepMap program should also be cited:
Arafeh, R., Shibue, T., Dempster, J.M. et al. The present and future of the Cancer Dependency Map. Nature Reviews Cancer 25, 59-73 (2025). https://doi.org/10.1038/s41568-024-00763-x