Figure 1.
This webpage is designed for the genome-wide visualization and analysis of methylation intensity (A, B, C). Methylation intensity is pre-calculated for a 100 bp bin size and is shown using a red gradient heatmap. A variety of genomic annotations and functional toolbars give users more options in browsing the webpage. Statistical methods were imbedded, including DMR analysis (A) and statistical calculation (C). Links to UCSC genome browser (D) and to gene view (E) are available for further analysis.
Figure 2.
This webpage is designed for visualization and analysis of methylation intensity at the gene level. In the toolbar, four layers of options are available to enable specific selections gene sets. Methylation intensities for promoter regions of genes (+/− 2 kb around TSS region) were pre-calculated and were shown using a red gradient heatmap. A white/green box on the side of gene symbol shows the promoter regions of this particular gene with or without CpG island(s). Clicking on the gene symbol on the left side of the heatmap panel will bring the user back to the genomic viewer centered on the selected gene, allowing visualization of detail methylation patterns.
Table 1.
Eight classes of gene set names and their sources.
Figure 3.
Discovery of tumor specific methylation profiles.
HOXB2 was hypermethylated in breast tumors compared with breast normal (A), while hypomethylated in endometrial cancer tumors compared with endometrial normal (B).
Figure 4.
Discovery of methylation correlated genes.
Gene set with similar methylation profiles of HOXB2 were found by choosing the “Correlated gene” gene sets in the gene centric view. Most of the genes are hypermethylated in breast tumors (blue dash box), and with no significant difference in endometrial samples (green dash box).
Figure 5.
Discovery of differentially methylated gene sets within a pathway.
The “Androgen-mediated Signaling” gene set which contains HOX cluster genes were selected as an example. Several genes within the blue dash box are hypermethylated in breast tumors compared to normal tissues, while others show no significant difference. For endometrial samples, no significant difference is found for any of the gene between tumors and normals.
Figure 6.
Visualization of DNA methylation and histone modification data.
The TSS region of DLC1 is used as an example. 4 samples were randomly selected by marking the check box on the right side of the webpage for breast samples (e.g., brn80, brt22, brt69 and brt37). The “full” option for every custom track and the Broad Histone tracks was selected for the comparison of DNA methylation and histone modification marks. Similar results were obtained as previous report [4]. An exception (the 3rd track, brt22) was found which shows patient specific patterns (A); and there was no increased methylation found for endometrial samples (B).