Integrative Bioinformatics and Machine Learning Analysis Identifies Novel Molecular Biomarkers in Prostate Adenocarcinoma.

Prostate adenocarcinoma is characterized by substantial inter-patient heterogeneity, limiting the clinical reliability of conventional diagnostic tools, including prostate-specific antigen testing. This limitation underscores the need for robust molecular biomarkers that may complement conventional diagnostic tools, highlighting the urgent need for biomarkers capable of enhancing diagnostic accuracy and enabling more precise risk stratification. In the present study, transcriptomic data from The Cancer Genome Atlas (TCGA) were analyzed using an integrative bioinformatics and machine learning pipeline., The proposed workflow was designed as a stepwise and reproducible biomarker prioritization framework in which differential expression analysis, functional enrichment, protein-protein interaction (PPI) based network interpretation, graph-convolutional feature selection, and hybrid ensemble machine learning were sequentially integrated. Differential gene expression analysis was combined with pathway enrichment (Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and Reactome), protein-protein interaction network construction, and graph-convolutional feature selection. Multiple machine learning algorithms, including Random Forest, Gradient Boosting Machine, Support Vector Classifier, Artificial Neural Network, and AdaBoost, were systematically evaluated. A hybrid ensemble model integrating Gradient Boosting Machine and Random Forest (GBM+RF) was subsequently developed. Model performance was assessed using accuracy, sensitivity, specificity, and area under the Receiver Operating Characteristic (ROC) and externally validated using the independent GSE14206 dataset. The analysis revealed a coordinated molecular pattern characterized by dysregulated cell cycle activity and enhanced interferon-mediated immune signaling. Protein-protein interaction analysis identified