Functional Interpretation of Differential Gene Expression in Cancer: From Lists to Mechanisms

High-throughput transcriptomic technologies have made differential gene expression analysis a cornerstone of cancer research by generating extensive lists of differentially expressed genes across tumor types and conditions. However, such lists provide limited biological insight without functional and mechanistic interpretation. This review examines the transition from descriptive gene expression profiles to a mechanistic understanding of cancer biology. We discuss integrative approaches that place expression changes within signaling pathways, transcriptional regulatory networks, and protein–protein interaction networks, thereby helping to identify functional modules and candidate upstream regulators. We emphasize the context-dependent nature of gene expression, which is shaped by genetic alterations, epigenetic landscapes, microenvironmental signals, and cellular heterogeneity. We also examine methodological advances, including gene set enrichment analysis, network-based modeling, and integration of genomic, epigenomic, proteomic, metabolomic, and single-cell transcriptomic data. Case studies across cancer types illustrate how mechanistic analyses can reveal context-specific transcriptional programs associated with oncogenic signaling, tumor suppression, metabolic reprogramming, epithelial–mesenchymal transition, and tumor–immune interactions. We highlight potential translational applications, including candidate biomarker discovery, prioritization of druggable targets, rational design of combination therapies, and investigation of therapeutic resistance. Finally, we discuss current challenges and emerging technologies, such as spatial transcriptomics and clustered regularly interspaced short palindromic repeats (CRISPR)-based perturbation screens, that are advancing the field toward dynamic, systems-level models of tumor biology. Integrating computational analyses with experimental validation can help translate transcriptomic data into clinically relevant hypotheses for precision oncology and personalized cancer therapy.