From chromosome to SNP: another way to look at the data.
In the above sections from 3.3 to 3.5 we discussed the most interesting annotation pathways to most WGA analyzers, i.e., the annotation for top hits, as well as the searching for specific genes and SNPs. Alternative to this, WGAViewer offers a more general and intuitive look at the WGA data. This pathway, as illustrated in Figure 3.6-1, starts from genome overview, goes through chromosome view and genic view, and finally annotates selected SNPs.
Figure 3.6-1. From chromosome to SNP.
Take our pre-annotation set “CHAVI_SETPOINT_SCIENCE.wr” as an example. Figure 3.6-2 shows a genome overview after this dataset is successfully loaded.
Figure 3.6-2. From chromosome to SNP: genome overview. (Click to enlarge)
Tab “Genome overview” (panel with “A” marked) plots P values as evenly-spaced lines. WGAViewer will automatically determine a resolution and only plots the lowest P values in ‘n' adjacent data points. In this tab panel, every data line will respond to mouse movement and will show a small stick presenting the SNP position and P value. Every chromosome label (circled and marked as “A”) will respond to mouse click and will bring the user interface into chromosome view (Figure 3.6-3). Alternative to this panel, the database plotter plots all data points (marked as “B”). Each portion of the plotting region can also respond to a mouse click, which will then result in an improved resolution in the database plotter window. Clicking on the “annotate” button in this database plotter window with a high enough resolution can also switch the user interface into chromosome view (Figure 3.6-3).
Figure 3.6-3. From chromosome to SNP: chromosome view. (Click to enlarge)
Either way, as a consequence, the chromosome view is then brought forward (Figure 3.6-3). The –logP lines in this panel are also evenly-spaced and can respond to mouse movement and click. One has the option to either drag the mouse and select a region, or type in the chromosome region into the text field in the tool bar and click on button “Display”, to get an improved resolution. With a reasonable resolution, for example, including around 200 SNPs as shown from Figure 3.6-3 (too many SNPs will take a long time to annotate, especially for LD calculation), one then may click the “Annotate” button to annotate this region.
Figure 3.6-4 shows the annotation results in genic view panel. The details of this panel have already been discussed (Figure 3.3.2.a-1). One has the options to either click on SNP P value lines and then click on item “Annotate SNP” in the pop-up menu, or select a SNP from a drop-down menu and click on “Annotate” button to annotate a SNP (circled in Figure 3.6-4). And as a consequence, SNP view panel (Figure 3.6-5) becomes the focus showing the annotation results, which then enables the further annotation for each HapMap SNPs, or one may go back to chromosome view or genic view to annotate other WGA SNPs. The details of SNP view have also been discussed (Figure 3.3.2.c-1).
Figure 3.6-4. From chromosome to SNP: genic view. (Click to enlarge)
Figure 3.6-5. From chromosome to SNP: SNP view. (Click to enlarge)