26Q1 DepMap Release Notes
MODEL ANNOTATIONS
DepMap Subtype Tree
The DepMap Subtype Tree has been updated in accordance with the October 9, 2025 OncoTree update, including a large resubtyping for the CNS/Brain lineage. To reflect these changes, we have re-annotated any model which was previously assigned a now obsoleted OncoTree code.
Please read OncoTree’s release notes here for more information on added/removed subtypes.
NEW CRISPR AND OMICS DATA
The DepMap team is excited to announce the addition of new genome-wide CRISPR screening and Omics data for 25 models across several cancer subtypes!
OTHER NEW DATASETS
HCMI TPM dataset in Celligner
We have added 591 models and 298 tumors from the Human Cancer Models Initiative (HCMI) into our Celligner visualization, using RNA-seq TPM quantifications from NCI’s Genomic Data Commons (GDC).
To harmonize the transcriptomic data from HCMI models with our DepMap models, HCMI TPM values were adjusted using a mean shift correction based on models common to both datasets. For each gene, we subtracted the HCMI-specific mean and added the corresponding DepMap mean. HCMI tumors are now available to view in Celligner.
Please note this dataset is not otherwise available on the DepMap portal.
Olink Proteomics dataset (harmonized_Olink_2023_best_dilution.csv)
We have profiled 161 cell lines covering 24 different cell line lineages using the Olink Explore HT platform. To learn more about Olink, please visit their website here.
Olink data is available in Data Explorer and as a separate downloadable file. Samples were run in three different dilutions, and one optimal dilution was selected for each protein independently. The data matrix is indexed by model_id, and each column corresponds to one protein, identified by UniProt ID. Some Models in this dataset do not have other omics or screen data available, so please refer to Models.csv for their metadata information if needed.
This dataset can be found for download under Harmonized Public Proteomics 26Q1 Files.
Sanger Proteomics dataset (harmonized_Sanger_MS_2022.csv)
Matrix of relative protein quantities from Gonçalves et al. 2022. The original data was downloaded from Cell Model Passports, but matches the data in the paper supplement. Please read the paper for more information about how this dataset was generated.
This dataset can be found for download under Harmonized Public Proteomics 26Q1 Files.
CRISPR PIPELINE UPDATES
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Updated Chronos library correction for genes not present in all CRISPR libraries
- Previously, Chronos performed library correction only on genes that are present in all CRISPR libraries present in the dataset. This strategy led to the presence of residual library effects for genes that only belong to a subset of libraries. In order to minimize the library batch effect present in CRISPRGeneEffect.csv and ScreenGeneEffect.csv, Chronos has been updated to perform library correction for genes that are present in more than one screen batch. The updated Chronos library correction does not affect the format of released files.
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Rescued screens: Three screens were previously dropped due to missing Copy Number data but are now again available on the portal:
- SC-001956.AV01, SC-001957.AV01, SC-001958.AV01
OMICS PIPELINE UPDATES
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Mutation Pipeline
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We’ve made the following changes to our mutation calling pipeline. For details, see 26Q1 mutation pipeline documentation
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Updates to variant filtering and calling
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Mutations in HLA genes are no longer considered hotspots
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NEW TOOLS
GeneTEA App Integration
We’ve added a new UI for allowing users to perform GeneTEA analyses into the portal! It is accessible from the “Tools” menu:
Or you can access it directly from Data Explorer, by selecting genes in a plot and seeing GeneTEA results in the lower right corner:
From there, you can navigate to the interactive UI via the “View in TEAparty” link.
OTHER PORTAL UPDATES
Context Manager and a replacement for “Cell Line Selector”
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A major update to Context Manager now allows for metadata types other than “Models” to be used when defining contexts. For example, you can now define a gene context, which comprises all genes on a particular chromosome arm.
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Also the tabular view of models with their properties has been moved into this new version of Context Manager. If you wish to see the full registry of models, you can define a context and click “View as table” at the bottom, and you’ll be shown a view which is analogous to the Cell Line Selector view from before.
New dose curve tab
The “Dose Curves” tab of compound pages have been updated to show dose curves across all cell lines in a single plot. One can highlight a context of interest and see how the response curves compare with the responses seen in all other lines.
“Screen metadata”
Previously in Data Explorer and Context Manager, data stored as a per-screen level was accessed by selecting “Screen metadata.” This label has now been changed to “CRISPR Screen”.
