# 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

![](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-8fc2dee750d8724b28bb148cba0491bb2c313f9c%2Fimage2017-12-26%2012_33_51.png?alt=media)

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).

![](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-9f89533575fa4969bdda8ac53552d8285362d910%2Fimage2017-12-26%2012_37_29.png?alt=media)

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)

![](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-9fd2a52570d83a1588cf2f705bd1f7e23897f0f5%2Fimage2017-12-26%2012_45_46.png?alt=media)

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 (![](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-8110271c2ae1416fc3c646fe751e86e4fd513d1f%2Fselection%20mode%20icon.png?alt=media)) for selection mode and (![](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-2fa4103bc9ebbaea62a5b3bbb91f4164df2cf189%2Fnavigation%20mode%20icon.png?alt=media)) 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 (![](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-25dba47cd7619ca2e185e22e00e0a26ef5bcca9c%2Fzoom%20control%20icons.png?alt=media)). View can be reset to the whole chromosome level using reset zoom (![](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-a684b58c76c09335c1506fdb6b1936bfbe1b0043%2Freset%20icon.png?alt=media)). 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](https://help.partek.illumina.com/partek-genomics-suite/tutorials/differential-methylation-analysis/optional-add-ucsc-cpg-island-annotations).

## Additional Assistance

If you need additional assistance, please visit [our support page](http://www.partek.com/support) to submit a help ticket or find phone numbers for regional support.