‘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 but complementary. For T21, both IPA and GSEA/DFLAT identified dysregulation of brain, cardiovascular, and integumentary system development. For TTTS, both analytic tools identified dysregulation of cell growth/proliferation, immune and inflammatory signaling, brain, and cardiovascular development. For maternal obesity, both tools identified dysregulation of immune and inflammatory signaling, brain and musculoskeletal development, and cell death. GSEA/DFLAT identified substantially more dysregulated biologic functions in fetuses of obese women (1203 vs 151). For all 3 datasets, GSEA/DFLAT provided more comprehensive information about brain development. IPA consistently provided more detailed annotation about cell death. IPA produced many dysregulated terms that pertained to cancer (14 in T21, 109 in TTTS, 26 in maternal obesity); GSEA/DFLAT did not.

Interpretation of the fetal amniotic fluid supernatant transcriptome depends on the analytic program, which suggests that >1 resource should be used. Within IPA, physiologic cellular proliferation in the fetus produced many “false positive” annotations that pertained to cancer, which reflects its bias toward adult diseases. This study supports the use of gene annotation resources with a developmental focus, such as DFLAT, for ‘omics studies in perinatal medicine.