TY  - JOUR
T1  - Interpreting Gene Essentiality across Biological Contexts: A Causal Framework for Separating Perturbation Effects, Compensatory Responses, and Environmental Dependencies in Functional Genomics
A1  - Michael Tan
A1  - Laura Fitzgerald
A1  - James Whitfield
JF  - Journal of Biochemical Technology
JO  - J Biochem Technol
SN  - 0974-2328
Y1  - 2026
VL  - 17
IS  - 4
DO  - 10.51847/f9gURdIGVM
SP  - 5
EP  - 13
N2  - Gene essentiality is often summarized as whether disruption of a gene reduces cellular or organismal fitness, yet functional-genomic evidence shows that this phenotype depends on the perturbation applied, the biological background in which it is imposed, the compensatory capacity of the system, and the environment in which fitness is measured. This article develops a causal account for interpreting context-dependent essentiality without treating screen-derived dependency scores as intrinsic, context-free properties of genes. Evidence from large-scale cancer dependency maps, cross-study CRISPR analyses, physiologic-medium screens, combinatorial perturbation studies, and in vivo functional genomics is organized around three separable components: the direct consequence of perturbing a gene, the compensatory or buffering response triggered by that perturbation, and modifiers arising from genetic background or environmental state. The framework additionally treats the observation process—perturbation modality, temporal window, assay design, and analytical model—as part of the causal interpretation problem. Gene essentiality is therefore most defensibly interpreted as a conditional relationship between a defined intervention and a fitness outcome in a specified biological and measurement context. This account provides a basis for distinguishing robust dependencies from context-limited vulnerabilities and for designing perturbation experiments that discriminate among competing causal explanations.
UR  - https://jbiochemtech.com/article/interpreting-gene-essentiality-across-biological-contexts-a-causal-framework-for-separating-perturb-ufl2ef94drfltxs
ER  -