Human Gene Set: GENES_CORRELATED_WITH_CDK6_DELETION
Standard name
GENES_CORRELATED_WITH_CDK6_DELETION
Systematic name
M50944
Brief description
Genes correlated with the sensitivity to CRISPR knockdown of gene CDK6 [GeneSymbol=CDK6]
Full description or abstract
The procedure to generate this gene set is as follows: we began by generating a CRISPR sensitivity vector using the negative relative cell viability readouts from the DepMap CRISPR screen (release 25Q3, Broad Institute) for gene CDK6. We aligned this dependency data with DepMap global mRNA expression data (CCLE mRNA, release 25Q3), retaining only the 1,106 cell lines present in both datasets. The overlapping samples were randomly partitioned into a Training Set (66%) and a Test Set (34%). Using an information-theoretic association metric, we quantified the association between the CRISPR dependency target and the mRNA expression of every gene in the training set. This process ranked genes based on how closely their expression aligned with the specific gene CDK6 CRISPR dependency. Subsequently, we performed a gene set optimization procedure. Using varying numbers of the top-ranked genes we constructed candidate gene signatures. We then computed the association of their ssGSEA-derived enrichment scores against the CRISPR target, and identified the gene set size that maximized the association score in the training data. This procedure defined the final genetic perturbation-based gene set for gene CDK6. Finally, we validated the gene set against the target in the test set to ensure it exceeded a minimum association threshold (0.20).
Creative Commons Attribution 4.0 International License (CC-BY-4.0)
The contents of this gene set are protected by copyright (c) 2004-2026 Broad Institute, Inc., Massachusetts Institute of Technology,
and Regents of the University of California, subject to the terms and conditions of the
Creative Commons Attribution 4.0 International License.
