WELCOME TO THE DIANA LAB TOOLS WEBPAGE

Lab Intro

Recent studies have unveiled the numerous roles of non-coding RNAs (ncRNAs) highlighting the biological significance of these previously 'overlooked' RNA species. NcRNAs and especially microRNAs (miRNAs) and, more recently, long ncRNAs (lncRNAs) are currently in the center of biological research; involved in a plethora of biological processes affecting cell homeostasis.

miRNAs are considered post-transcriptional gene regulators enabling translational repression, mRNA degradation and gene silencing thus playing a major role in gene expression. They bind on their target usually by partial or complete base pairing on specific miRNA recognition elements (MREs) on mRNA as well as other non-coding RNA sequences such as lncRNAs.

Recent findings have also revealed some of the cellular mechanisms involving lncRNAs. For instance, lncRNAs have been shown to be associated to chromatin remodeling; structural scaffolding of nuclear protein substructures; cell cycle regulation; binding to Polycomb repressive complexes and even interacting with miRNA molecules and regulate gene expression.

Aim of DIANA Tools is to provide algorithms, databases and software for interpreting and archiving data in a systematic framework ranging 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 ncRNAs in various diseases and pathways.

The arsenal of DIANA Tools ranges from target prediction algorithms (microT v4 and microT-CDS), databases of experimentally verified miRNA targets on coding and non-coding RNAs (TarBase v7.0 and LncBase) to software capable of identifying potentially altered molecular pathways by the expression of a single or multiple miRNAs (mirPath). In addition, the newly developed Web Server (v5.0) supports a series of sophisticated workflows enabling users without the necessary bioinformatics infrastructure to perform advanced multi-step functional miRNA analyses.

Currently active projects of the DIANA-lab group include:

MicroRNA target prediction

microT-CDS: DIANA-microT-CDS is the 5th version of the microT algorithm. It is specifically trained on a positive and a negative set of miRNA Recognition Elements (MREs) located in both the 3'-UTR and CDS regions. DIANA-microT-CDS provides a significant increase in sensitivity compared to the previous version (65% vs 52%), when compared against experimental proteomics data. DIANA-microT-CDS can be accessed from the following address: http://www.microrna.gr/microT-CDS.

microT v4: DIANA-microT-ANN is the 4th version of the microT algorithm. The server contains predictions for four species and supports miRBase 18 and Ensembl 69. It can support different prediction algorithms and exploits high throughput experimental data. DIANA-microT-ANN can be accessed from the following address: /DianaTools/index.php?r=microtv4/index.

Database of experimentally supported microRNA targets

TarBase v7.0 is the largest available manually curated target database, indexing more than 65,000 miRNA-gene interactions, 16.5-175-fold more than any other available implementation. The database includes targets derived from specific, as well as high throughput experiments, such as microarrays and proteomics. Specific attention was paid in the inclusion of targets derived from sequencing experiments, such as HITS-CLIP and PAR-CLIP. TarBase hosts data derived from 3 CLIP-Seq and 12 Degradome-Seq studies, significantly more than any other available database. TarBase v7.0 can be accessed from the following address: http://www.microrna.gr/tarbase.

Incorporating microRNAs in pathways

mirPath is the new version of DIANA-miRPath web server, which was redesigned from the ground-up. DIANA-miRPath performs miRNA pathway analysis, providing accurate statistics, while being able to accommodate advanced pipelines. miRPath can utilize predicted miRNA targets provided by the DIANA-microT-CDS algorithm and/or experimentally validated miRNA interactions derived from DIANA-TarBase v6.0. DIANA-miRPath v2.0 can be accessed from the following address: http://www.microrna.gr/miRPathv2.

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 nucleotide long motifs (hexamers) in the 3'UTR sequences of genes. DIANA-mirExTra can be accessed from the following address: http://diana.cslab.ece.ntua.gr/hexamers/.

DIANA-web server 5.0

The new DIANA web server was completely redesigned. DIANA web server v5.0 has innate support to the latest Ensembl (v.69), miRBase version (miRBase 18) and nomenclature, while keeping backwards compatibility with all previous miRBase versions for selected tools, such as DIANA-TarBase. All available tools have been extended to support by default Drosophila melanogaster and C. elegans (as well as Homo sapiens and Mus Musculus). DIANA web server supports also a series of sophisticated workflows enabling users without the necessary bioinformatics infrastructure to perform advanced multi-step functional miRNA analyses.