Data-Mining Approach on Transcriptomics and Methylomics Placental Analysis Highlights Genes in Fetal Growth Restriction.
data mining
intrauterine growth restriction
methylomics
multi-omics
text-mining
transcriptomics
Journal
Frontiers in genetics
ISSN: 1664-8021
Titre abrégé: Front Genet
Pays: Switzerland
ID NLM: 101560621
Informations de publication
Date de publication:
2019
2019
Historique:
received:
10
08
2019
accepted:
25
11
2019
entrez:
31
1
2020
pubmed:
31
1
2020
medline:
31
1
2020
Statut:
epublish
Résumé
Intrauterine Growth Restriction (IUGR) affects 8% of newborns and increases morbidity and mortality for the offspring even during later stages of life. Single omics studies have evidenced epigenetic, genetic, and metabolic alterations in IUGR, but pathogenic mechanisms as a whole are not being fully understood. An in-depth strategy combining methylomics and transcriptomics analyses was performed on 36 placenta samples in a case-control study. Data-mining algorithms were used to combine the analysis of more than 1,200 genes found to be significantly expressed and/or methylated. We used an automated text-mining approach, using the bulk textual gene annotations of the discriminant genes. Machine learning models were then used to explore the phenotypic subgroups (premature birth, birth weight, and head circumference) associated with IUGR. Gene annotation clustering highlighted the alteration of cell signaling and proliferation, cytoskeleton and cellular structures, oxidative stress, protein turnover, muscle development, energy, and lipid metabolism with insulin resistance. Machine learning models showed a high capacity for predicting the sub-phenotypes associated with IUGR, allowing a better description of the IUGR pathophysiology as well as key genes involved.
Identifiants
pubmed: 31998361
doi: 10.3389/fgene.2019.01292
pmc: PMC6962302
doi:
Types de publication
Journal Article
Langues
eng
Pagination
1292Informations de copyright
Copyright © 2020 Chabrun, Huetz, Dieu, Rousseau, Bouzillé, Chao de la Barca, Procaccio, Lenaers, Blanchet, Legendre, Mirebeau-Prunier, Cuggia, Guardiola, Reynier and Gascoin.
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