Networks are displayed graphically as gene/genes products (nodes) and the biological relationships between the nodes (edges). All edges are supported by at least one reference from
the literature, or from canonical information stored in the Ingenuity Pathways Knowledge Base. In addition, IPA computes a score for each network according to the fit of the user’s set of significant genes. The score, representing the – log(P-value), indicates the likelihood selleck products of the Focus Genes in a network from Ingenuity Knowledge Database being found together randomly. We identified X chromosome sites that were consistently hypermethylated (n = 18, Table 1) and hypomethylated (n = 25, Table 2) in affected twins. Within the 5-kb window sampled for each X-linked gene, most of the differentially methylated regions (DMRs) were located in promoter regions or CpG islands while two hypermethylated (48980151–48980208 and 104355356–104355413) and six hypomethylated (103883076–103883125, Wnt signaling 47226194–47226247, 134532227–134532289, 134532327–134532376, 134532427–134532476, 134532627–134532676) DMRs were found downstream
of the transcription start sites. In all cases, DMRs were associated with known genes and we noticed that IL1RAPL2 was found in both lists (the two hypermethylated sites are downstream of the hypomethylated one). In some cases, multiple DMRs belong to the same gene (as in the case of hypomethylated peaks Org 27569 134532227–134532289, 134532327–134532376, 134532427–134532476 and 134532627–134532676 onto gene DDX26B) or a specific site is located in a CpG island of
a bidirectional promoter for two different genes (i.e. hypomethylated peak 152712287–152712338 for genes SSR4 and IDH3G). Three hypomethylated peaks are associated with intergenic single-nucleotide polymorphisms (SNP), with peak 13087308–13087357, including SNP rs61677044, peak 13087708–13087757 falling in a region 150 bp downstream from SNP rs16978681, peaks 126140539–126140588 and 126140739–126140788 mapping to a SNP-rich region. Genes identified by the hypermethylated and hypomethylated sites encode for proteins that are illustrated in Tables 3 and 4, respectively. The 26 proteins include transcription factors, membrane and soluble enzymes, surface antigens and translocation proteins while in some cases proteins are currently defined only structurally, but not functionally. We explored possible functional relationships between the 26 genes using the IPA Knowledge Database. Unsupervised IPA network analysis identified a single cluster of 25 genes that included seven of our 26 genes and 18 additional genes, which was unlikely to occur by chance (P = 10−13). The plausible biological network generated is shown in Fig.
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