Additional file 1 of Maternal obesity and gestational diabetes reprogram the methylome of offspring beyond birth by inducing epigenetic signatures in metabolic and developmental pathways
Creators: name: Alba-Linares, Juan José
name: Pérez, Raúl F.
name: Tejedor, Juan Ramón
name: Bastante-Rodríguez, David
name: Ponce, Francisco
name: Carbonell, Nuria García
name: Zafra, Rafael Gómez
name: Fernández, Agustín F.
name: Fraga, Mario F.
name: Lurbe, Empar
Publisher: name: figshare
Year: 2023
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 1: Supplementary Information and Supplementary Figures S1–11. Figure S1. Barplots depicting the average blood cell-type composition for each combination of group (Control, Obese, Obese+Diab) and time point (t0, t6, t12), inferred via the Houseman algorithm from methylation data. Figure S2. Violin plot showing the magnitude of change of those DMPs common to common 0&gt;6 and 6&gt;12 which had the same direction of change at both time points. The magnitude of change is measured as the absolute β-value difference in the average methylation values of each CpG between the longitudinal groups. The P-value from a Wilcoxon rank sum test is shown. Figure S3. Boxplots showing examples of genes that accumulate a high number of hypermethylation alterations (FDR&lt;0.05) during the first year of development. Figure S4. Upset plots depicting intersections of significant results (FDR&lt;0.05) for Chemical and Genetic Perturbations (CGP), Gene Ontology Biological Process (GOBP) and Reactome (REACT) gene set enrichment analyses. Figure S5. Boxplots showing examples of genes that accumulate a high number of hypomethylation alterations (FDR&lt;0.05) during the first year of development. Figure S6. Venn diagrams indicating (A) the overlap of DMPs between all comparisons (Ob.C, ObDia.C, ObDia.Ob) in terms of hypermethylation DMPs and hypomethylation (FDR&lt;0.05) and (B) the overlap of CpGs belonging to DMRs (Sidak P&lt;0.05) between the same comparisons. Figure S7. Network showing the similarities found in the ObDia.C comparison with respect to the pathways found enriched (unadjusted P&lt;0.05) in the significant DMR analyses. Blue clusters relate to hypomethylation alterations and red clusters to hypermethylated DMRs. Figure S8. Boxplots showing examples of DMRs that are hypermethylated in the obesity and/or obesity+diabetes groups (Sidak P-value&lt;0.05). Figure S9. Boxplots showing some examples of DMRs that are hypomethylated in the obesity and/or obesity+diabetes groups (Sidak P-value&lt;0.05). Figure S10. (a) Venn diagram showing the intersection between the DMPs that change at least in one longitudinal comparison preserving the direction of the change (Dev) and the CpGs found in the ObDia.C DMRs. (b) Venn diagrams depicting the overlaps between aforementioned CpGs, separated by the direction of the methylation change. (c) Sankey diagram describing the distribution of Dev DMPs when considering the changes between ObDia and C subjects. (d) Sankey diagram showing the distribution of those Dev DMPs that experience hyper- and hypo- changes between ObDia and C subjects. (e) Bubble plots showing the top 5 most significant GO BP and CGP gene sets (FDR&lt;0.05) for the Dev DMPs based on their methylation patterns between ObDia and C subjects. Figure S11. (a) Sankey diagram describing the distribution of CpGs coming from ObDia.C DMRs when considering their methylation differences during development. (b) Sankey diagram showing the distribution of ObDia.C DMR CpGs excluding those that do not change during development. (c) Bubble plots showing the top 5 most significant GO BP and CGP gene sets (unadjusted P&lt;0.05) for the ObDia.C DMR CpGs based on their methylation patterns across development.