If it's not working for you, please let us know: parkerlab-software at umich.edu.
Most recent browsers should work fine. We've noticed that Firefox, much as we love it, can be a little sluggish
relative to the others, so if it's too slow for you, please try another browser. Chrome, Safari and Edge seem
to be faster, at least for this.
How to use it
At any time, you can reset the plot to its initial state with the Reset plot button.
If you're interested in a particular gene, type part of its name or Ensembl ID in the text input labeled Gene.
You can filter the variants by chromatin state, by biotype, by iESI (islet expression specificity index), or
whether an ATAC-seq footprint was observed at the variant location. Simply click any filter in the
list. Hovering over a filter will preview the variants it matches. Clicking a filter again will remove it
from the active filters. You can select multiple filters to combine sets of variants. Selecting all filters
in a filter category is equivalent to selecting none.
The plot itself
Hovering over any shape in the plot will display a tooltip containing the variant's details.
Clicking any shape in the plot will add its details to the table below the plot labeled Variant Details. The Gene column in that table contains links to the Ensembl page for the variant's gene. The Position column
contains links to 100kb windows centered on the variants in this UCSC Genome Browser session. If you click a variant by mistake, you can remove it from the table by clicking the Remove button in the last column.
You can zoom the plot with your mouse wheel or trackpad. Zooming in separates the variants, making them easier to
click. You can also pan the plot by dragging with the mouse. At any time, you can get back to the starting zoom and
position by clicking the Reset plot button.
Islet expression specificity index
The islet expression specificity index (iESI) is a measure of islet-specific gene expression, with a range from 0 to 1. Here we partition the scores into deciles. A gene with an iESI score in decile 10 is expressed highly and specifically in islets compared to other tissue types.
You should be able to print the page at any time using your browser's default print dialog. If you notice
problems with the output, please let us know.
You can save the state of the explorer at any time with the Save button at the top right. In the resulting dialog, enter a name to save the session under, and it will be added to the Sessions table. In that table, you can press Load to load a saved session, or Remove to delete them.
At any time you can press the Share button at top right to get a URL to share your current session. It has to be copied to the clipboard manually, for browser security reasons; just press the Copy to clipboard button or use the keyboard: Command-C on Macs, Control-C elsewhere.