Protocol for integrative transcriptomic/metabolomic analysis: A case study on factors influencing the oyster-POMS disease

Deciphering the molecular mechanisms underlying complex biological interactions requires comprehensive approaches that capture these interactions across multiple regulatory and functional levels. Here, we present a protocol applied to the host-pathogen-environment interactions underlying Pacific oyster mortality syndrome (POMS) in Magallana gigas . We describe steps from individual transcriptomic and metabolomic workflows using WGCNA and FELLA packages, to their integration in a biologically meaningful framework. This protocol aims to move omics integration beyond statistical correlations toward functional enrichment with cross-validation at the system level. For complete details on the use and execution of this protocol, please refer to Duperret et al. 1