Table 1.
Demographics and RAND-36 results of subjects selected for the study.
Figure 1.
Distribution of differentially methylated regions in CFS.
Distribution of hyper- and hypo-methylated CpG regions in CFS patients compared to healthy control subjects according to (a) genic location 1500 bp and 200 bp relative to the transcription start site (TSS), in the 5′ UTR, 3′ UTR, and within gene bodies and (b) location relative to CpG islands, including 2 kb upstream and downstream of CpG islands (N, S Shore respectively), and 2 kb upstream and downstream of CpG shores (N, S Shelf respectively). No significant differences were found within CpG islands.
Figure 2.
Validation of microarray data by pyrosequencing.
Validation of significant methylation differences identified by microarray (450 K) by pyrosequencing (PS), showing the average methylation level of CpG sites within the following genes (probe ID, genic location): (a) LY86 (cg02212836, first exon), (b) HIPK3 (cg25600606, gene body), and (c) LCN2 (cg14615559, TSS200). * = FDR<0.05, 450 K; * = p<0.05, PS, Wilcoxon rank-sum test. Error bars represent the standard error of the mean.
Figure 3.
Clustering of DAVID GO results.
Network map showing the clustering of DAVID GO results as produced by the Enrichment Map plugin in Cytoscape 2.8.2. Significant GO term clusters were named according to textual attributes generated by the WordCloud plugin. Node size (red circles) corresponds to the number of genes within the GO terms. Edge thickness (green lines) represents genes in common between GO terms.
Figure 4.
Distribution of differentially methylated sites in CFS according to GO clusters and functional relevance.
Relative proportions of hyper- and hypo-methylated CpG sites between CFS patients and healthy control subjects for genes associated with the immune cell regulation cluster group (immune GO) compared to all four GO term cluster groups (all GO). Results are shown for each genic region, consisting of promoter regions within 1500 bp and 200 bp of the transcription start sites (TSS), gene regulatory elements (regulatory: TSS1500, TSS200, 5′ UTR, 3′ UTR), the coding regions of genes (gene body), as well as all regions combined (total: regulatory, gene body). * = p<0.0125, Pearson Chi-Squared Test.
Table 2.
Immune cell regulation GO cluster.
Table 3.
Immune cell regulation GO cluster genes.