Protocol for integrative transcriptomic/metabolomic analysis: A case study on factors influencing the oyster-POMS disease
Year: 2026
Type: article
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
Source: STAR Protocols
Authors: Leo Duperret, Alejandro Valdivieso, Bruno Petton, Benjamin Morga, Nicole Faury, Julien de Lorgeril, Charlotte Corporeau, Lionel Degremont, Sylvain Henry, Andrei Turtoi, Juliette Pouzadoux, Océane Romatif, Gaelle Courtay, Cristián J. Monaco, Eve Toulza, Arnaud Lagorce, Jeremie Vidal-Dupiol, Guillaume Mitta
Institutions: Centre National de la Recherche Scientifique, Université de Perpignan, Ifremer, Université de Bretagne Occidentale, Institut Universitaire Européen de la Mer, Laboratoire des Sciences de l'Environnement Marin, Institut de Recherche pour le Développement, University of New Caledonia, Gouvernement de la Nouvelle-Calédonie, Inserm, Université de Montpellier, BioCampus Montpellier, Institut de Recherche en Cancérologie de Montpellier, University of French Polynesia
Language: English
Subfield: Global and Planetary Change
Field: Environmental Science
Domain: Physical Sciences
Open Access status: gold
Estimated APC paid: $1,550
Funder: Agence Nationale de la Recherche
OpenAlex ID: W7218772732