Guide to RNA-Get (gene expression)

The RNA-get interface allows you to look up the expression values for all the genes in every RNA-based assay available on the ENCODE portal. Currently the different assays that you can visualize the expression values for include different flavors of RNA-seq as well as PAS-seq.

By default the page displays the expression values of REM1. In order to search for your gene of interest on this interface:

  1.  Type the gene name or gene id of your interest in the search box located on the top left corner. The search box has an auto-completion feature which allows the users to get a list of hits that correspond to the keyword that is being typed.  
  2. Next, you can choose to view the results in either TPM or FPKM units using the drop-down next to search box.
  3. Press the search button to view your search results.
  4. By default the search will return all the available entries.  If you would like to narrow down your search results further, you can select the different facets located below the search box (Annotation, Assay, Classification, Organ, Sex, System and Biosample). Selecting the values on the different facets will narrow down your table to include just those specific selections.

By default the users will be able to visualize the first 100 entries per page and the users can toggle between the different pages using top right corner page navigative buttons. Each row represents a unique experiment and the expression value of the gene is represented in the column "Counts (TPM)" or "Counts (FPKM)". The different columns in the table are sortable (in both ascending and descending orders). One can perform sorting by clicking on the triangular button next to the column title. The columns provide useful information about the experiment from which the expression value of that gene is extracted from. The experiment and file columns contain the ENCODE experiment ID (ENCSR ID) and file ID (ENCFF ID) respectively, which may be clicked to navigate to the individual experiment and file pages.

For more information on the RNA-Get API, click here.