View Mutations on 3D protein structures (Xena -> MuPIT)
Figure. Xena Browser link-out to MuPIT 3D mutation view. On the left of the figure is Xena mutation column view of ERBB2 somatic mutations from the TCGA breast cancer cohort (https://xenabrowser.net/heatmap/?bookmark=6098aca9a00041d6271f18f2b471a241). User clicking on the MuPIT link-out menu (similar to how xena links out to Tumor Map), it will send all the mutations' genomic positions as well as their recurrence p values to the MuPIT display. On the right side of the figure, MuPIT displays mutations in various size of bright green spheres. Large spheres for recurrent mutations. Size of the mutation spheres are determined by recurrence p values. The MuPIT display shows these ERBB2 somatic mutations cluster around the ERBB2 active site (ATP binding site in blue and proton acceptor site in teal).
Access this tool by going to our Visualization tab and following the wizard to enter your mutation data of interest into the Visual spreadsheet, which is our default view. Please make sure to choose 'Somatic mutation (SNP and small INDEL)', not 'Somatic non-silent mutation (gene-level)'.
Once you have the mutation data you're interested in, click the caret menu at the top of the column and chose 'MuPIT View'. This will send your mutation data to MuPIT and open their viewer in a new tab.