Visualize methylation at each locus

Partek Genomics Suite enables you to visualize each probe and compare the methylation between the groups at a single CpG site level.

Right click row 5. SBNO2 in the LCLs_vs_B_Cells_CpG_Islands spreadsheet
Select Browse to Location from the pop-up menu

Figure 1. Browsing to location from spreadsheet with differentially expressed genes

The Chromosome View tab will open, zoomed in to the selected CpG locus in SBNO2 (Figure 2).

Figure 2. Viewing location in Genome Viewer

The Chromosome View visualization is composed of a series of tracks corresponding to annotation files and data files.

RefSeq Transcripts 2017-05-02 (hg19) (+): transcripts coded by the positive strand
RefSeq Transcripts 2017-05-02 (hg19) (-): transcripts coded by the negative strand
Regions: by default, difference in methylation (M-value) between the groups
Heatmap (1/mvalue): M values for all the samples
Barchart (Methylation): methylation level in M value of the selected sample (to select a sample, click on a heat map)
Heatmap (Methylation Tutorial): Beta values for all the samples
Barchart (Methylation): methylation level in Beta value of the selected sample (to select a sample, click on a heat map)
Cytoband: cytobands of the current chromosome
Genomic Label: coordinates on the current chromosome

To modify a track, select it in the Tracks panel to bring up its configuration options panel below the Tracks panel. Let's modify a few tracks to improve our visualization of the data.

Select the Regions track, opens to Profile tab
Select Color tab
Set Color bars by to Difference (LCLs vs. B cells) (Description)
Select Apply to change

This will color regions by up or down methylated.

Select the Heatmap (1/mvalue)
Select Remove Track
Select Bar Chart (Methylation) located directly below the Regions track
Select Remove Track

We can now more clearly see the Difference in M values for the region in the Regions track, the heatmap of beta values in the Heatmap track, and the beta value for the loci of the selected sample in the Bar Chart track.

Select a sample on the heatmap to view its beta value in the Bar Chart track (Figure 3)

Figure 3. Modify the tracks of the Genome Viewer to facilitate visual analysis

The New Track button allows new tracks to be added to the viewer, while the Remove Track button removes the selected track from the viewer. Tracks can be reordered by selecting a track in the Tracks panel and dragging it up or down to move it in the list. In the Chromosome View, select () for selection mode and () for navigation mode. In navigation mode, left-click and draw a box on any track to zoom in. All tracks are synced and will zoom together. Zooming can also be controlled using the interface in the lower right-hand corner of the tab (). View can be reset to the whole chromosome level using reset zoom (). Searching for a gene or transcript in the position box will also zoom directly to its location.

The available tracks can be supplemented with a special annotation file that can be built using a UCSC annotation file as the basis. Building and viewing the UCSC annotation file is available as an optional section of the tutorial, Optional: Add UCSC CpG island annotations.

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