DIANA LAB (c) 2008DIANA LAB (c) 2008DIANA LAB (c) 2008DIANA LAB (c) 2008
     B.S.R.C. Alexander Fleming
 

THIS SITE IS NO LONGER SUPPORTED


The new and improved web interface of DIANA tools can be accessed through here.


 
   
 WELCOME TO THE DIANA LAB WEBPAGE

Lab Intro
Computational predictive models are a key element of current systems biology. 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.

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.

Currently active projects of the DIANA-lab group include:

MicroRNA target prediction

DIANA-microT 3.0 is an algorithm based on several parameters calculated individually for each microRNA and it combines conserved and non-conserved microRNA recognition elements into a final prediction score. The program reports a signal to noise ratio and a precision score which help in the evaluation of the significance of the predicted results. The web server provides extensive information for predicted microRNA:target gene interactions providing extensive connectivity to online biological resources. Target gene and microRNA functions may be elucidated through automated bibliographic searches and functional information is accessible through 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.

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. 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.

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.


Database of experimentally supported microRNA targets
TarBase5.0 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 1300 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.
 
   
   
 LATEST LAB PUBLICATIONS

papadopoulos g, alexiou p, maragkakis m, reczko m, hatzigeorgiou a. (2009) diana-mirpath: integrating human and mouse micrornas in pathways., bioinformatics. ,[epub ahead of print] PubMed

maragkakis m, reczko m, simossis va, alexiou p, papadopoulos gl, dalamagas t, giannopoulos g, goumas g, koukis e, kourtis k, vergoulis t, koziris n, sellis t, tsanakas p, hatzigeorgiou ag. (2009) diana-microt web server: elucidating microrna functions through target prediction., nucleic acids res. ,[epub ahead of print] PubMed

megraw m, pereira f, jensen st, ohler u, hatzigeorgiou ag (2009) a transcription factor affinity based code for mammalian transcription initiation, genome res ,19(4): ,644-56.. PubMed

papadopoulos gl, reczko m, simossis va, sethupathy p, hatzigeorgiou ag. (2009) the database of experimentally supported targets: a functional update of tarbase., nucleic acids res. ,(database issue) ,d155-8. PubMed

 
   
   
 
LAB MEMBERS

Lab Head
hatzigeorgiou, artemis (phd)
Lab Members
alexiou , panagiotis (msc)
maragkakis , manolis
papadopoulos, giorgos l.
Lab Visitors
reczko , martin (phd)
riback, joshua