Metabolism, gene regulation, and biological processes of the human body happen in molecular pathways, and any disruption in the pathways may directly lead to diseases. Molecular signatures can help get a closer look into cell biology and the mechanisms of human diseases. Therefore, the aim of the research is to discover molecular signatures and pathways which are active unusually in the NPC tissues to outline a few of the essential pathogenesis involved. Thus, genome-wide expression profiling of the NPC tissue is analyzed to identify pathways and distinguish them based on their functionality. Gene-disease association data is used to describe how molecular pathways of nasopharynx cancer are linked to different diseases. By analyzing the gene-disease associations, 392 genes are found out that are common with NPC and other diseases. This study also finds out that neuronal disorders and cancer diseases categories are closely associated with NPC. Protein–protein interaction (PPI) networks which are crucial for understanding cell physiology in both normal and disease states are formed to identify the shared protein groups of various diseases. Overall, this study identifies biomarkers (e.g., hub proteins, TFs, and miRNAs) that regulate gene expression and control important biological processes and molecular pathways of NPC with other diseases. This study can assist further studies to identify the NPC biomarkers and potential drug targets. Determination of the right targets will be helpful for a combined therapeutic approach.