Under the extreme climate conditions, the events of crop damage are increasing. There is an urgent need to breed stress-tolerant varieties. Flooding stress on different growth stages of soybean can negatively affect seed germination, plant growth, flowering, yield and quality. These impacts are linked with the ability of plant adaptation or tolerance to flooding stress, which involves with complex physiological traits, metabolic pathways, biological processes, molecular components and morphological adaptations. However, investigating mechanisms of flooding stress tolerance is time-consuming. In the present study, we conducted systems biology approaches to identify pathways and network hubs linking flooding stress tolerance. We previously identified 63 prioritied flooding tolerance genes (FTgenes) of soybean from multiple dimensional data sources using large-scale data mining and gene prioritization methods.