Protocol for integrative transcriptomic/metabolomic analysis: A case study on factors influencing the oyster-POMS disease
Abstract
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
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Authors: Léo Duperret, A. Valdivieso, Bruno Petton, Benjamín Morga, Nicole Faury, Julien de Lorgeril, Charlotte Corporeau, Lionel Dégremont, S. Henry, Andrei Turtoï, Juliette Pouzadoux, Océane Romatif, Gaëlle Courtay, Cristián J. Monaco, Eve Toulza, Arnaud Lagorce, Jérémie Vidal‐Dupiol, Guillaume Mitta
Institutions: Inserm, Centre National de la Recherche Scientifique, Institut de Recherche pour le Développement, Université de Bretagne Occidentale, Université de Montpellier, Institut de Recherche en Cancérologie de Montpellier, Institut Universitaire Européen de la Mer, Laboratoire des Sciences de l'Environnement Marin, Université de Perpignan, Ifremer, University of New Caledonia, University of French Polynesia, BioCampus Montpellier, Gouvernement de la Nouvelle-Calédonie