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Summary: Investigating network behavior from host-pathogen interactions is challenging. Here, we present the deep-learning-based protocol to construct an immune-related gene network and list the genes involved in the defense response of host to specific biotic stress. The protocol includes the steps to pre-process the interaction pairs and expression profile of plants treated with pathogen/control, feed as input for DLNet algorithm to rank genes based on their contribution to data classification. The top-ranked genes are subjected to module and enrichment analysis.For complete details on the use and execution of this protocol, please refer to Kumar et al. (2022).1 : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.