DIANA-microT Web server upgrade supports Fly and Worm miRNA target prediction and bibliographic miRNA to disease association

Abstract

microRNAs (miRNAs) are small endogenous RNA molecules that are implicated in many biological processes through post-transcriptional regulation of gene expression. The DIANA-microT Web server provides a user-friendly interface for comprehensive computational analysis of miRNA targets in human and mouse. The server has now been extended to support predictions for two widely studied species: Drosophila melanogaster and Caenorhabditis elegans. In the updated version, the Web server enables the association of miRNAs to diseases through bibliographic analysis and provides insights for the potential involvement of miRNAs in biological processes. The nomenclature used to describe mature miRNAs along different miRBase versions has been extensively analyzed, and the naming history of each miRNA has been extracted. This enables the identification of miRNA publications regardless of possible nomenclature changes. User interaction has been further refined allowing users to save results that they wish to analyze further. A connection to the UCSC genome browser is now provided, enabling users to easily preview predicted binding sites in comparison to a wide array of genomic tracks, such as single nucleotide polymorphisms. The Web server is publicly accessible in www.microrna.gr/microT-v4.

Figure 1.

An example of a tag cloud for hsa-miR-1 showing relevant disease associated MeSH terms.

Figure 2.

Example of a DIANA-microT Web server results page. Balloons indicate and explain important features of the results page. ‘Related diseases’ tag cloud contains links to PubMed and specifies all papers which associate the particular disease with the corresponding miRNA. The field ‘PubMed links’ provides automated bibliography searches based only on the name of miRNAs, protein coding genes or the combination of both. The ‘UCSC graphic’ link presents the predicted binding sites in a UCSC genome browser window along with tracks such as SNPs and repeat elements. The left side of the page is devoted to the administration of the user personal space and reports their latest searches and bookmarks.

Figure 3.

Graphic presentation of the changes involved in the history of miRNA mmu-miR-455. Initially, MIMAT0003485 was presented in version 8.1 as mmu-miR-455 but its name changed consecutively to mmu-miR-455-5 p in version 8.2 and mmu-miR-455-star (mmu-miR-455*) in version 10.0. Similarly, MIMAT0003742 was first presented in version 8.2 as mmu-miR-455-3 p, while in version 10.0, its sequence changed and it was renamed to mmu-miR-455.