depmap

When to Use This Skill

Use DepMap when:

• Target validation: Is a gene essential for survival in cancer cell lines with a specific mutation (e.g., KRAS-mutant)?
• Biomarker discovery: What genomic features predict sensitivity to knockout of a gene?
• Synthetic lethality: Find genes that are selectively essential when another gene is mutated/deleted
• Drug sensitivity: What cell line features predict response to a compound?
• Pan-cancer essentiality: Is a gene broadly essential across all cancer types (bad target) or selectively essential?
• Correlation analysis: Which pairs of genes have correlated dependency profiles (co-essentiality)?

Dependency Scores

Score	Range	Meaning
Chronos (CRISPR)	~ -3 to 0+	More negative = more essential. Common essential threshold: −1. Pan-essential genes ~−1 to −2
RNAi DEMETER2	~ -3 to 0+	Similar scale to Chronos
Gene Effect	normalized	Normalized Chronos; −1 = median effect of common essential genes

Key thresholds:

• Chronos ≤ −0.5: likely dependent
• Chronos ≤ −1: strongly dependent (common essential range)

Cell Line Annotations

Each cell line has:

• DepMap_ID: unique identifier (e.g., ACH-000001)
• cell_line_name: human-readable name
• primary_disease: cancer type
• lineage: broad tissue lineage
• lineage_subtype: specific subtype