AIM AND BACKGROUND: Epicardial adipose tissue (EAT), adjacent to the myocardium, plays a role in coronary artery disease (CAD), though its thrombotic mechanisms remain unclear. This study aimed to identify CAD-specific thrombotic messenger RNAs (mRNAs) and their regulatory microRNAs (miRNAs) and long noncoding RNAs (lncRNAs) using expression analysis, network modeling, and clustering approaches. MATERIALS AND METHODS: Differential gene expression analysis was performed using the GSE64554 dataset (p < 0.05), identifying genes dysregulated in CAD. Thrombosis-related genes were retrieved from GeneCards and intersected with CAD-associated genes. Protein-protein interaction (PPI) networks were constructed to determine key hub genes. MicroRNAs and long noncoding RNA analyses were conducted to identify regulatory modules. Reverse transcription-quantitative polymerase chain reaction (RT-qPCR) was used to validate key miRNA expression in plasma and saliva samples from CAD patients (n = 30) and healthy controls (n = 30). RESULTS: A total of 840 genes were upregulated in CAD, with 85 overlapping thrombosis-related genes identified. Network analysis highlighted five key thrombosis-CAD hub genes involved in immune response, cytokine signaling, and signal transduction. miRNA profiling revealed 82 downregulated miRNAs in CAD, many targeting these hub genes. Of 1,122 regulatory modules analyzed, HIF1A, CTNNB1, and CCL5 were identified as central regulators. Integration of lncRNA data further emphasized hsa-miR-641 as a key regulatory miRNA, significantly downregulated in both plasma and saliva samples from CAD patients, as confirmed by RT-qPCR. CONCLUSION: This study identifies key thrombotic genes and regulatory modules in EAT, emphasizing the role of immune and signaling pathways in CAD progression. The consistent downregulation of hsa-miR-641 and its detectability in plasma and saliva support its potential as a reliable noninvasive diagnostic biomarker. CLINICAL SIGNIFICANCE: hsa-miR-641 can serve as a non-invasive biomarker for early detection of CAD using saliva and plasma. It may also aid in risk assessment and guide targeted therapeutic strategies.