Example 1: m6A modifications found in HEK293T cells from 2 replicates treated with GLORI.

Click the "Search modifications" tab, and select the organism and assembly we want to work with on the right side of the page.

We can now construct the query. Sci-Modom currently allows to select datasets by modification and method.

We select the chosen dataset from "Available dataset (set A)". For this example, we limit our search to modifications found in the 3'UTR. As we don't want to limit our search to a set of candidate genes, we ignore this option. We now expand the combinatorial search settings by clicking on "Combinatorial search", and repeat the same procedure, this time selecting "replicate 2". As we are interested in modifications found in both replicates, we use the "AND" set operation.

After a few seconds, the results page is displayed. A button at the top of the page allows you to download the complete results in EUF file format (in progress). To optimise loading times, the results page only displays the top 100 hits, a button on the bottom of the page allows you to load more results. Public data can be viewed on the USCS Genome Browser.

Example 2: Y modifications found in both my results and a published dataset

This time, we use the "Browse" button to "submit" our own results (BED or EUF), and select the organism and assembly we want to work with on the right side of the page.

We move immediately to the "Combinatorial search", and select "set B" from the available dataset. As we are interested in modifications found in both our results and the published BID-seq results (Mouse Heart tissue), we use the "AND" set operation.