How to download essential genes from DepMap?

Essential genes are those required for a cell’s survival and proliferation. Identifying them is crucial for understanding core biological processes and uncovering potential therapeutic targets, especially in cancer. The DepMap (Dependency Map) project profiles genetic dependencies across hundreds of cancer cell lines using CRISPR screens, providing a rich resource to study gene essentiality.

Common Essential Genes?

DepMap classifies genes as common essential if they are consistently required for the survival of a wide range of cell lines. These genes typically perform fundamental cellular functions such as:

• RPL3 — encodes a ribosomal protein critical for protein synthesis.
• PCNA — a key player in DNA replication and repair.
• PSMB5 — a proteasome subunit involved in protein degradation.
• CCT8 — essential for proper folding of cytoskeletal proteins.

These genes are so crucial that their loss is generally lethal across most cancer types, making them less ideal for targeted therapy (due to potential toxicity), but vital for understanding core cellular machinery.

How to Download Common Essential Genes from DepMap

To access the list of essential genes:

1. Go to the DepMap gene dependency summary download link: https://depmap.org/portal/api/download/gene_dep_summary. This file contains gene-level dependency scores aggregated across cell lines.
2. Filter the data: Only keep rows where the “Dataset” column is “DependencyEnum.Chronos_Combined”.
3. Use the “Common Essential” column to identify genes that passed DepMap’s stringent threshold for essentiality. These will be marked as “True”

Step 1:

Step : 2

Step: 3

Reference:

1. https://forum.depmap.org/t/common-essential-gene-list/2576