What are the procedures involved in the unbiased empirical sampling based approach?

The unbiased empirical sampling method is used to estimate the null distribution of the target genes as selected based on the input miRNAs. The procedures can be divided into the following steps:

  1. A list of miRNAs of the same size are randomly selected from all the miRNAs with known targets in the database;
  2. The functional annotations (i.e. GO or KEGG) are then performed for the list;
  3. The process is repeated 1000 times (default);
  4. Compare the GO or KEGG pathway hits. The empirical p values (Emp. p) are calculated as the proportion of overlaps (with pathways or GO terms) from 1000 random process that equal or larger than the original. A p value < 0.001 will be reported if no results from random process are better than the original.