Human Gene Set: GENES_CORRELATED_WITH_PPM1D_DELETION


Standard name GENES_CORRELATED_WITH_PPM1D_DELETION
Systematic name M50936
Brief description Genes correlated with the sensitivity to CRISPR knockdown of gene PPM1D [GeneSymbol=PPM1D]
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 PPM1D. 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 PPM1D 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 PPM1D. Finally, we validated the gene set against the target in the test set to ensure it exceeded a minimum association threshold (0.20).
Collection C9: Computational Perturbation Signature
Source publication  
Exact source  
Related gene sets  
External links
Filtered by similarity ?
Source species Homo sapiens
Contributed by Pablo Tamayo (MSigDB Team)
Source platform or
identifier namespace		 HUMAN_GENE_SYMBOL
Dataset references  
Download gene set format: grp | gmt | xml | json | TSV metadata
Compute overlaps ? (show collections to investigate for overlap with this gene set)
Compendia expression profiles ? NG-CHM interactive heatmaps
(Please note that clustering takes a few seconds)
GTEx compendium
Human tissue compendium (Novartis)
Global Cancer Map (Broad Institute)
NCI-60 cell lines (National Cancer Institute)

Legacy heatmaps (PNG)
GTEx compendium
Human tissue compendium (Novartis)
Global Cancer Map (Broad Institute)
NCI-60 cell lines (National Cancer Institute)
Advanced query Further investigate these 55 genes
Gene families ? Categorize these 55 genes by gene family
Show members (show 55 source identifiers mapped to 55 genes)
Version history 2026.1.Hs: First Introduced.


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.

See the full MSigDB license terms here.