The medicinal effect of a drug acts through a series of genes, and the pathological mechanism of a disease is also related to genes with certain biological functions. However, the complex information between drug or disease and a series of genes is neglected by traditional message passing methods. In this study, we proposed a new framework using two different strategies for gene-drug/disease and drug-disease networks, respectively. We employ long short-term memory (LSTM) network to extract the flow of message from series of genes (gene path) to drug/disease. Incorporating the resulting information of gene paths into drug-disease network, we utilize graph convolutional network (GCN) to predict drug-disease associations. Experimental results showed that our method GeneDR (gene-based drug repurposing) makes better use of the information in gene paths, and performs better in predicting drug-disease associations.