The pathway not taken: understanding 'omics data in the perinatal context

American Journal of Obstetrics and Gynecology
Andrea G EdlowDiana W Bianchi

Abstract

'Omics analysis of large datasets has an increasingly important role in perinatal research, but understanding gene expression analyses in the fetal context remains a challenge. We compared the interpretation provided by a widely used systems biology resource (ingenuity pathway analysis [IPA]) with that from gene set enrichment analysis (GSEA) with functional annotation curated specifically for the fetus (Developmental FunctionaL Annotation at Tufts [DFLAT]). Using amniotic fluid supernatant transcriptome datasets previously produced by our group, we analyzed 3 different developmental perturbations: aneuploidy (Trisomy 21 [T21]), hemodynamic (twin-twin transfusion syndrome [TTTS]), and metabolic (maternal obesity) vs sex- and gestational age-matched control subjects. Differentially expressed probe sets were identified with the use of paired t-tests with the Benjamini-Hochberg correction for multiple testing (P < .05). Functional analyses were performed with IPA and GSEA/DFLAT. Outputs were compared for biologic relevance to the fetus. Compared with control subjects, there were 414 significantly dysregulated probe sets in T21 fetuses, 2226 in TTTS recipient twins, and 470 in fetuses of obese women. Each analytic output was unique...Continue Reading

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Citations

Feb 4, 2016·BJOG : an International Journal of Obstetrics and Gynaecology·A G EdlowD W Bianchi
Oct 26, 2016·Prenatal Diagnosis·Lillian M ZwemerDiana W Bianchi
Mar 7, 2017·American Journal of Obstetrics and Gynecology·Roberto RomeroAdi L Tarca
Dec 15, 2017·CPT: Pharmacometrics & Systems Pharmacology·Sara K QuinneyDavid M Haas
Jul 23, 2018·Genetics in Medicine : Official Journal of the American College of Medical Genetics·Neeta L Vora, Lisa Hui

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