Phenotype Association Tools in Galaxy

PolyPhen-2 results

We find 104 SNPs that are predicted to be damaging by PolyPhen-2 (blue arrow), including one of our two coding disease SNPs (not shown). For small datasets like this, you can display the entire contents by clicking on the eye icon in the history panel. (The columns do not line up in this view because the data is tab-separated and the values in each column are not all of the same length.)

In the blue box you can see that we now have UniProt IDs for many of the genes associated with these variants. We can look for pathways associated with the genes by using the CTD tool, however that tool requires HUGO/NCBI identifiers rather than UniProt IDs for its input, so first we will download a file from UCSC to map between the identifiers (red arrow in the tool panel).

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