Web Based Tools

New microRNA Web Resources

by Chris on June 11, 2010

MAGIA - (miRNA and genes integrated analysis) is a novel web tool for the integrative analysis of target predictions, miRNA and gene expression data. MAGIA is divided into two parts: the query section allows the user to retrieve and browse updated miRNA target predictions computed with a number of different algorithms (PITA, miRanda and Target Scan) and Boolean combinations thereof. The analysis section comprises a multistep procedure for (i) direct integration through different functional measures (parametric and non-parametric correlation indexes, a variational Bayesian model, mutual information and a meta-analysis approach based on P-value combination) of mRNA and miRNA expression data, (ii) construction of bipartite regulatory network of the best miRNA and mRNA putative interactions and (iii) retrieval of information available in several public databases of genes, miRNAs and diseases and via scientific literature text-mining. MAGIA is freely available for Academic users at http://gencomp.bio.unipd.it/magia.

Sales G, Coppe A, Bisognin A, Biasiolo M, Bortoluzzi S, Romualdi C. (2010) MAGIA, a web-based tool for miRNA and Genes Integrated Analysis. Nucleic Acids Res [Epub ahead of print]. [article]

MiRror – A combinatorial analysis web tool for ensembles of microRNAs and their targets.

The miRror application provides insights on microRNA (miRNA) regulation. It is based on the notion of a combinatorial regulation by an ensemble of miRNAs or genes. miRror integrates predictions from a dozen of miRNA resources that are based on complementary algorithms into a unified statistical framework. For miRNAs set as input, the online tool provides a ranked list of targets, based on set of resources selected by the user, according to their significance of being coordinately regulated. Symmetrically, a set of genes can be used as input to suggest a set of miRNAs. The user can restrict the analysis for the preferred tissue or cell-line. miRror is suitable for analyzing results from miRNAs profiling, proteomics and gene expression arrays. AVAILABILITY: http://www.proto.cs.huji.ac.il/mirror.

Friedman Y, Naamati G, Linial M. (2010) MiRror: A combinatorial analysis web tool for ensembles of microRNAs and their targets. Bioinformatics [Epub ahead of print]. [abstract]

SeqBuster  - a highly versatile and reliable web-based toolkit to process and analyze large-scale small RNA datasets. SeqBuster integrates multiple analyses modules in a unique platform and constitutes the first bioinformatic tool offering a deep characterization of miRNA variants (isomiRs). The application of SeqBuster to small-RNA datasets of human embryonic stem cells revealed that most miRNAs present different types of isomiRs, some of them being associated to stem cell differentiation. The exhaustive description of the isomiRs provided by SeqBuster could help to identify miRNA-variants that are relevant in physiological and pathological processes. SeqBuster is available at http://estivill_lab.crg.es/seqbuster.

Pantano L, Estivill X, Martí E. (2010) SeqBuster, a bioinformatic tool for the processing and analysis of small RNAs datasets, reveals ubiquitous miRNA modifications in human embryonic cells. Nucleic Acids Res 38(5), e34.  [article]

 WMD Version 3 Released – WMD3 is a web app for the automated design of artificial microRNAs.  Artificial microRNAs (amiRNAs) are 21mer small RNAs, which can be genetically engineered and function to specifically silence single or multiple genes of interest in more than 90 plants, according to the previously determined parameters of target gene selection. It uses your favorite gene(s), which you want to silence, and designs 21mer amiRNA sequences. You will retrieve oligo sequences to express the small RNA from endogenous miRNA precursors.

Schwab R, Ossowski S, Riester M, Warthmann N, Weigel D. (2006) Highly specific gene silencing by artificial microRNAs in Arabidopsis. Plant Cell 18(5), 1121-33. [article]

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Web-Based Tools for MicroRNA Analysis from Deep Sequencing Data

by Chris on December 23, 2009

mirTools – a web server for microRNA profiling and discovery based on high-throughput sequencing data.

Classification of the large-scale short reads into known categories, such as known miRNAs, non-coding RNA, genomic repeats or coding sequences.

Providing a detailed annotation information of known miRNAs, such as miRNA/miRNA*, absolute/relative reads count and the most abundant tag.

Discovery of the novel miRNAs from the high-throughput sequencing technology.

Identification of the differentially expressed miRNAs according to read tag counts (the number of reads for each tag reflects relative express level).

miRDeep – Discovering known and novel miRNAs from deep sequencing data

The miRDeep package was developed to discover active known or novel miRNAs from deep sequencing data (Solexa/Illumina, 454, …). The package consists of everything you need to analyze your own deep sequencing data after removal of ligation adapters: a number of scripts to preprocess the mapped data, and the core miRDeep algorithm that will analyze and score these data.

deepBase – a database for deeply annotating and mining deep sequencing data

a novel database, developed to facilitate the comprehensive annotation and discovery of small RNAs from transcriptomic data. The current release of deepBase contains deep sequencing data from 185 small RNA libraries from diverse tissues and cell lines of seven organisms: human, mouse, chicken, Ciona intestinalis, Drosophila melanogaster, Caenhorhabditis elegans and Arabidopsis thaliana. For the purpose of comparative analysis, deepBase provides an integrative, interactive and versatile display. A convenient search option, related publications and other useful information are also provided for further investigation. [click to continue…]

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