Evidence map›Paper›PMID 42828751›Full record

ArticleSTAR protocols2026

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

Leo Duperret, Alejandro Valdivieso, Bruno Petton, Benjamin Morga, Nicole Faury, Julien de Lorgeril, Charlotte Corporeau, Lionel Degremont, Sylvain Henry, Andrei Turtoi and 8 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in STAR protocols, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

18 authors.

Leo DuperretIHPE, University of Perpignan Via Domitia, CNRS, IFREMER, University of Montpellier, Perpignan, France. Electronic address: duperretleo@gmail.com.
Alejandro ValdiviesoIHPE, University of Montpellier, CNRS, IFREMER, University of Perpignan Via Domitia, Montpellier, France.
Bruno PettonIfremer, University of Brest, CNRS, IRD, LEMAR, IUEM, Plouzané, France.
Benjamin MorgaIfremer, ASIM, La Tremblade, France.
Nicole FauryIfremer, ASIM, La Tremblade, France.
Julien de LorgerilENTROPIE, IFREMER, Université de Nouvelle-Calédonie, Université de La Réunion, IRD, Nouvelle-Calédonie, 98800 Nouméa, France.
Charlotte CorporeauIfremer, University of Brest, CNRS, IRD, LEMAR, IUEM, Plouzané, France.
Lionel DegremontIfremer, ASIM, La Tremblade, France.
Sylvain HenryPlatform for Translational Oncometabolomics, Biocampus, CNRS, INSERM, Université de Montpellier, Montpellier, France.
Andrei TurtoiPlatform for Translational Oncometabolomics, Biocampus, CNRS, INSERM, Université de Montpellier, Montpellier, France; Tumor Microenvironment and Resistance to Therapy Lab, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Montpellier, France; Gunma University, Initiative for Advanced Research (GIAR), Maebashi, Gunma, Japan.
Juliette PouzadouxIHPE, University of Montpellier, CNRS, IFREMER, University of Perpignan Via Domitia, Montpellier, France.
Océane RomatifIHPE, University of Montpellier, CNRS, IFREMER, University of Perpignan Via Domitia, Montpellier, France.
Gaelle CourtayIHPE, University of Montpellier, CNRS, IFREMER, University of Perpignan Via Domitia, Montpellier, France.
Cristián J MonacoIfremer, University of Brest, CNRS, IRD, LEMAR, IUEM, Plouzané, France; Ifremer, IRD, Institut de Louis-Malardé, Université Polynésie française, UMR SECOPOL, Taravao, Tahiti, French Polynesia.
Eve ToulzaIHPE, University of Perpignan Via Domitia, CNRS, IFREMER, University of Montpellier, Perpignan, France.
Arnaud LagorceIHPE, University of Perpignan Via Domitia, CNRS, IFREMER, University of Montpellier, Perpignan, France.
Jeremie Vidal-DupiolIHPE, University of Montpellier, CNRS, IFREMER, University of Perpignan Via Domitia, Montpellier, France.
Guillaume MittaIfremer, IRD, Institut de Louis-Malardé, Université Polynésie française, UMR SECOPOL, Taravao, Tahiti, French Polynesia.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

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.

Indexed as

BioinformaticsMetabolomicsRNAseq

Identifiers

PMID42828751
PMCPMC13659763

What OpenQuestion holds

Textmetadata
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.