Tests for association of SNP with gene expression
WGAViewer offers a convenient tool to easily test association between SNP genotypes and gene expression data, quantified in immortalized B-lymphocytes, using the databases from the Sanger Institute GENEVAR project (Stranger et al. 2005; Stranger et al. 2007) and the HapMap project (The International HapMap Consortium. 2007) .
To do this, click on menu “Tools ->GENEVAR: test for genotype-expression association ” and this will activate a dialog for inputs (Figure 3.8.1-2). Two types of inputs are supported: (1) directly typing in SNP rs# and gene symbol, as shown from Figure 3.11.1-1; or (2) selecting a text file containing the SNP-gene pairs between which association will be tested, for example, as shown in Box 3.11.1-1.
Figure 3.11.1-1. Test for genotype-gene expression association (Click to enlarge)
Click on button “Perform test”. Figure 3.11.1-2 shows the results based on inputs from Figure 3.11.1-1. Click on the “Stats” tab for a sheet of statistics, or click on the “Graph” tab for graphs (Figure 3.11.1-3). If multiple SNP-gene pairs were entered (from an input file), one has the option to select to particular genes and SNPs from two drop-down menus (circled in Figure 3.11.1-3).
Figure 3.11.1-2. Text-based results for test for genotype-gene expression association (Click to enlarge)
Figure 3.11.1-3. Graphical results for test for genotype-gene expression association (Click to enlarge)