DIANA Lab microRNA Databases and Tools

Category Genomics>Gene Expression Analysis/Profiling/Tools, Cross-Omics>Pathway Analysis/Gene Regulatory Networks/Tools and Cross-Omics>Knowledge Bases/Databases/Tools

Abstract The focus of the DIANA Lab is on the development of algorithms, databases and tools for interpreting and archiving genomic data in the framework of a systemic analysis.

Current emphasis is on the analysis of microRNA (miRNA) and protein coding genes.

MiRNAs are recently identified to be very abundant in mammalian organisms and play a key role in regulating development.

Computational predictive models are a key element of current systems biology and comprehensive models work and integrate data at various levels of biological detail.

Therefore the activities of the DIANA lab range from the analysis of expression regulation from deep sequencing data, the annotation of miRNA regulatory elements and targets to the interpretation of the role of miRNAs in various diseases.

DIANA Lab microRNA Databases and Tools include:

1) TarBase 5.0 - Database of experimentally supported microRNA targets --

TarBase 5.0 is a database which houses a manually curated collection of experimentally supported microRNA targets, in several animal species of central scientific interest, plants and viruses.

Even though several computational programs exist to predict miRNA targets, there is a need for a comprehensive collection and description of miRNA targets with experimental support.

The current version of TarBase includes more than 1,300 experimentally supported targets and each target site is described by the miRNA that binds it, the gene in which it occurs, the nature of the experiments that were conducted to test it, the sufficiency of the site to induce translational repression and/or cleavage, and the paper from which all these data were extracted.

Additionally, the database is functionally linked to several other relevant and useful databases such as Ensembl, Hugo, UCSC and SwissProt.

2) miRGen 2.0 - a database of microRNA genomic information and regulation --

miRGen 2.0 is an integrated database of miRNA gene transcripts, Transcription Factor Binding Sites, miRNA expression profiles and Single Nucleotide Polymorphisms (SNPs) associated with miRNAs.

miRGen 2.0 aims to provide comprehensive information about the position of human and mouse microRNA coding transcripts and their regulation by transcription factors, including a unique compilation of both predicted and experimentally supported data.

Expression profiles of microRNAs in several tissues and cell lines, single nucleotide polymorphism locations, microRNA target prediction on protein coding genes and mapping of miRNA targets of co-regulated miRNAs on biological pathways are also integrated into the database and user interface.

The miRGen database will be continuously maintained.

3) DIANA-microT - MicroRNA target prediction --

4) DIANA-mirExTra -- Analysis of expression data for microRNA function --

DIANA-mirExTra is an algorithm that can identify microRNA effects to the Expression levels of protein-coding Transcripts, based on the frequency of six (6) nucleotide long motifs (hexamers) in the 3' UTR sequences of genes.

Additional features include the combination of multiple hexamers corresponding to the same microRNA sequence, use of evolutionary conservation between human and mouse to increase robustness and correction of microarray data for single nucleotide compositional bias.

Direct links to further functional analysis of produced results based on DIANA-mirPath are provided for all results.

5) DIANA-mirPath - Incorporating microRNAs in pathways --

DIANA-mirPath is a web-based computational tool developed to identify molecular pathways potentially altered by the expression of single or multiple microRNAs.

The software performs an enrichment analysis of multiple microRNA target genes comparing each set of microRNA targets to all known KEGG pathways.

The combinatorial effect of co-expressed microRNAs in the modulation of a given pathway is taken into account by the simultaneous analysis of multiple microRNAs.

The graphical output of the program provides an overview of the parts of the pathway modulated by microRNAs, facilitating the interpretation and presentation of the analysis results.

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