MiRNA And Genes Integrated Analysis (MAGIA)

Category Genomics>Gene Expression Analysis/Profiling/Tools

Abstract 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 (2) parts:

1) The Query section allows the user to retrieve and browse updated miRNA target predictions for human miRNAs, based on a number of different algorithms (PITA, miRanda, and TargetScan), with the possibility of combining them with Boolean operators.

2) The Analysis section comprises a multi-step procedure for:

Note: Step-by-step tutorial pages and sample data sets are provided to the user to easily introduce you to the use of the tool.

MAGIA Query --

The Query section of MAGIA allows the user to search for target predictions of specific miRNAs obtained through PITA, miRanda, or TargetScan or combinations thereof (as stated above…), setting cutoffs on prediction scores.

Target prediction algorithms have been selected according to their different strategies: sequence similarity (miRanda), sequence similarity with conservation (TargetScan), and sequence similarity with free energy minimization (PITA).

The manufacturers run each of these algorithms on their servers to update predictions every six (6) months.

The query output is a table including, for all considered miRNAs, the list of predicted target genes or transcripts with different prediction scores according to the method(s) chosen by the user.

The same information may be downloaded as a text file for processing and further elaboration.

MAGIA Analysis --

The Analysis pipeline is composed of three (3) different steps through which MAGIA refines target predictions using miRNA and mRNA gene expression data:

1) Selection of the organism, the gene or transcript annotation (EntrezGene, RefSeq, ENSEMBL gene or transcript) and the integration method or the relatedness measure;

2) Choice of target prediction algorithms, their score cut-offs and Boolean combinations; and

3) Upload of two (2) matrices representing mRNA and miRNA normalized expression profiles. MAGIA takes into account two (2) different experimental designs:

The tool employs a meta-analysis approach based on a P-value combination in the first case, while one of four (4) different measures of relatedness can be adopted for the analysis of matched profiles: Spearman and Pearson correlation, mutual information, and a variational Bayesian model.

Computational intensive calculations of MAGIA analyses are carried out by a multi-core cluster.

MAGIA Input files --

The third step of the MAGIA analysis pipeline takes as input two (2) expression matrices (in the tab-delimited format) with genes and miRNAs on the rows and samples on the columns.

When profiles are matched, the names of the columns of mRNA and miRNA data sets should correspond exactly, while in the non-matched-case the columns labels should represent sample classes: samples belonging to the same class should have the same label.

The first column of both matrices should represent miRNA and gene IDs.

MAGIA allows EntrezGene or Ensembl IDs for genes and RefSeq or Ensembl IDs for transcripts, while miRNA IDs must represent miRBase-compliant mature miRNA identifiers.

Expression matrices should be pre-processed and a filtering procedure for the removal of invariable (‘flat’) expression profiles is highly recommended.

A series of quality checks are performed during the upload.

MAGIA Output and links to other database resources --

MAGIA reports results in a web page containing different sections.

For the top 250 most probable functional miRNA-mRNA interactions according to the association measure selected by the user, the interactive bipartite regulatory network obtained through the analysis is reported along with the corresponding browsable table of relationships.

It gives the user a hyperlink allowing the functional enrichment analysis by the DAVID web tool - (see G6G Abstract Number 20263), on the desired number of target genes.

The tool also provides the complete list of the predicted interactions, ranked by statistical significance, computed from the integrated expression data analysis.

Such information is given as HTML tables and as two (Cytoscape-compliant) flat files for network reconstruction.

Each mRNA, miRNA or miRNA-mRNA interaction can be further investigated by the user and used for different queries.

In particular, each gene is linked to EntrezGene, and the ArrayExpress Atlas databases - (see G6G Abstract Number 20012), each miRNA is linked to miRNA2disease and miRecords.

Furthermore, to allow efficient and systematic retrieval of statements from Medline (PubMed), MAGIA directly links the results to PubFocus and EbiMEd for a text-mining search, using genes and miRNAs as keywords.

MAGIA Bi-partite networks visualizations --

The miRNA and gene bipartite network is rendered using the Graphviz open source graph visualization software.

Each node of the network can be selected and the user is directly linked to the corresponding miRNA/gene full interactions results.

Thus, the user is allowed to ‘walk through the network’ following miRNA and gene interactions.

The complete list of significant interactions can be downloaded as a tab-delimited text file that can be imported into Excel or Cytoscape - (see G6G Abstract Number 20092), to allow further processing.

System Requirements

Contact manufacturer.

Manufacturer

Manufacturer Web Site MiRNA And Genes Integrated Analysis (MAGIA)

Price Contact manufacturer.

G6G Abstract Number 20648

G6G Manufacturer Number 104245