Identifying Choroidal Neovascularization-Associated Genes with GenePlexus in a Protein–Protein Interaction Network

Choroidal neovascularization (CNV) is a common and serious complication in various retinal diseases that involves the growth of new blood vessels from the choroid into the subretinal space, leading to a visual threat. Its underlying mechanism has not been fully uncovered. Discovering new genes related to CNV is an important way to reveal its molecular mechanisms. In this study, we used DisGeNET as the initial data source to identify genes related to CNV. The gene cluster method and additional screening tests were designed to explore the genetic landscape related to CNV. Our comprehensive analysis revealed many genes with high confidence, specifically identifying novel candidates that traditional topological methods missed. Notably, we identified SERPINE1, COL1A1, and ANGPT1 as unique gene signatures using our network embedding approach. Functionally, SERPINE1 regulates the plasminogen activation system to control proteolytic balance, COL1A1 maintains the structural integrity of the extracellular matrix during invasion, and ANGPT1 is critical for the maturation and stabilization of nascent vessels. Meanwhile, some genes were also identified by other methods, such as MMP2, a regulator of extracellular matrix degradation. The newly found genes are essential for understanding the process that initiates CNV.