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. 2009 Jul;37(Web Server issue):W273-6.
doi: 10.1093/nar/gkp292. Epub 2009 Apr 30.

DIANA-microT web server: elucidating microRNA functions through target prediction

M Maragkakis  1 , M Reczko, V A Simossis, P Alexiou, G L Papadopoulos, T Dalamagas, G Giannopoulos, G Goumas, E Koukis, K Kourtis, T Vergoulis, N Koziris, T Sellis, P Tsanakas, A G Hatzigeorgiou
Affiliations

DIANA-microT web server: elucidating microRNA functions through target prediction

M Maragkakis et al. Nucleic Acids Res. 2009 Jul.

Abstract

Computational microRNA (miRNA) target prediction is one of the key means for deciphering the role of miRNAs in development and disease. Here, we present the DIANA-microT web server as the user interface to the DIANA-microT 3.0 miRNA target prediction algorithm. The web server provides extensive information for predicted miRNA:target gene interactions with a user-friendly interface, providing extensive connectivity to online biological resources. Target gene and miRNA functions may be elucidated through automated bibliographic searches and functional information is accessible through Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. The web server offers links to nomenclature, sequence and protein databases, and users are facilitated by being able to search for targeted genes using different nomenclatures or functional features, such as the genes possible involvement in biological pathways. The target prediction algorithm supports parameters calculated individually for each miRNA:target gene interaction and provides a signal-to-noise ratio and a precision score that helps in the evaluation of the significance of the predicted results. Using a set of miRNA targets recently identified through the pSILAC method, the performance of several computational target prediction programs was assessed. DIANA-microT 3.0 achieved there with 66% the highest ratio of correctly predicted targets over all predicted targets. The DIANA-microT web server is freely available at www.microrna.gr/microT.

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Figures

Figure 1.
Figure 1.
DIANA-microT web server results page. The key features have been marked in the figure and are explained below. (1) Gene names and corresponding links to UniProt (protein information) and iHOP (functional and bibliographic information). (2) KEGG pathways in which the gene of interest is involved. (3) MiRNA names and corresponding links to miRBase (sequence information) and iHOP. (4) A graph showing the SNR of the miRNA. The SNR is calculated by the DIANA-microT algorithm and is based on a comparative analysis of the real miRNA versus a set of mock miRNAs. (5) The prediction score. Higher miTG scores correspond to higher possibility of correct prediction. (6) SNR score of the interaction. Greater values correspond to better distinction from the mock background. This attribute must be examined in combination with the SNR diagram provided for each miRNA. (7) The precision score of the interaction. This score ranges from 0 to 1, and it estimates the significance of the prediction. (8) Literature links that perform an automated search in PubMed for the gene, the miRNA or for the combination of the two. (9) Binding site info: (a) binding type indicates the number of the binding nucleotides in the 5′-end of the miRNA; (b) UTR position indicates the position of the binding site on the 3′-UTR; (c) score indicates the contribution of each binding site to the overall miTG score; and (d) conservation indicates the number of species in which the binding site is conserved. (10) This field indicates if the interaction may be found in the database of experimentally supported targets (TarBase) or if it has additionally been predicted by another target prediction program (TargetScan or Pictar). (11) Additional binding site info: (a) position on chromosome shows the position of the binding site on the chromosome; (b) conservation info indicates the species in which the binding site is conserved; and (c) graphic representation of the miRNA binding on the 3′-UTR.
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