Supplementary figures
Figure S1: Diagnostic plots for microarray data quality control. A) Signal density plots for
all the arrays in the analysis. Signal distribution for each microarray is indicated by blue and red
curves for samples belonging to the LG-SF and LG-SC groups, respectively. Plots are based in
the full probe data sets (n=4,212,009 probes). B) Distribution of microarray signal intensities
before (left plot) and after (right plot) quantile normalization. Signal distribution for each
microarray is indicated by blue and red boxes for samples belonging to the LG-SF and LG-SC
groups, respectively. C) Correction of signal intensity distribution biases by quantile
normalization. Signal intensity distributions according to GC content and position in the
sequence before (left plots) and after (right plots) quantile normalization are shown.
Figure S2: DMRs associated with genes that are main nodes of gene networks. Genome
browser images showing the location of the DMRs for the Irs1 (panel A) and Apoe (panel B)
genes. These genes were identified as main nodes in functional gene networks and showed
significantly higher DNA methylation in the LG-SF and LG-SC groups, respectively. Location
of transcripts, CpG islands, DMRs and normalized signals are shown as in Figure 3.
Figure S3: DMRs associated with genes that have reported functions that are altered in
metabolic syndrome. Genome browser images showing the location of the DMRs for the Cartpt
(panel A) and Akt2 (panel B) genes. These genes have functions altered in metabolic syndrome
and showed significantly higher DNA methylation in the LG-SF and LG-SC groups,
respectively. Location of transcripts, CpG islands, DMRs and normalized signals are shown as in
Figure 3.
Supplementary Tables
Table S1: Primer sequences for Pparg locus analysis.
Table S2: List of DMRs and associated transcripts and genes.
Table S3: Candidate genes selected for pathway and gene network analysis.
Table S4: Canonical pathways overrepresented in DMR associated genes with higher
methylation in the LG-SF group.
Table S5: Canonical pathways overrepresented in DMR associated genes with higher
methylation in the LG-SC group.
Table S6: Ingenuity Pathway Analysis toxicity lists overrepresented in DMR associated genes
with higher methylation in the LG-SF group.
Table S7: Ingenuity Pathway Analysis toxicity lists overrepresented in DMR associated genes
with higher methylation in the LG-SC group.