A miRNA gene (top) is controlled by several TFs whose binding sites (TFBSs) are located near the TSS of this gene. When transcribed, the miRNA gene produces a long pri-miRNA molecule. The pri-miRNA molecule is cleaved by Drosha and yields the pre-miRNA stem-loop (hairpin) structure. The enzyme Dicer cleaves the loop part of the hairpin and produces the miRNA-miRNA* duplex. One chain of the miRNA duplex is incorporated into the RISC complex and can regulate mRNA translation by binding in a sequence specific manner to the 3′UTR region of mRNAs. In this example, the miRNA (produced after a TF binds to its promoter) regulates the translation of the promoter in a typical negative feedback control loop.

The miRGen database schema. TFs (top right) bind through TF binding sites to miRNA genes. miRNA genes (top) contain miRNA hairpins that signify the genomic location of the mature miRNA-miRNA* duplex. miRNA hairpins are processed into mature miRNAs. Usually, one miRNA hairpin produces two mature miRNAs, but a mature miRNA can be produced by more than one hairpin in different genomic locations. Both TFBSs and miRNA hairpins are genomic features that can contain SNPs. Mature miRNAs are associated with their expression levels in different tissues and cell types.

The user is able to query the database either by miRNA name, or by the name of the TF of interest. When a miRNA search is performed (Figure 3a), all distinct locations on the genome (hairpins) that could code for this miRNA are returned, and the user can see details for any of the possible overlapping transcripts identified for each location, usually predicted by different papers. Each transcript tab contains information about TFBSs located from 5 kb upstream to 1 kb downstream of the transcript start. Additionally, information on the expression levels of the mature miRNA are displayed as a heat map. Searching for a TF of interest (Figure 3b) returns all miRNA coding genes for which at least one binding site for this TF is found. Information on the gene, the TFBSs, and the mature miRNAs coded for by the gene can be seen in tabs. All instances of TFBSs and miRNA hairpins are associated with corresponding SNPs mapping on their genomic locations. For all transcripts, the literature source of the gene is displayed, the identification of the TSS (experimental if the TSS was identified in the paper, computational if it was calculated by computational means and first miRNA if the start of the first miRNA serves as a substitute for an unknown TSS), and whether the gene is intragenic or is co-expressed with a protein-coding gene.