a M@IA module

MIRna @Nd Transcription factor @nalysis Network

MIR@NT@N is an integrative approach based on a meta-regulation network model including TFs, miRNAs and genes, and provides a user-friendly graph-based application connected to a large scale database.

In order to identify and analyse molecular interaction networks within a given biological context, MIR@NT@N predicts regulatory networks and sub-networks including conserved motifs, feedback and feed-forward loops.

Connect to M@IA to access MIR@NT@N
Use "Guest" account without password

MIR@NT@N Overview - Network analysis including TFs, miRNAs and genes

Focus on actors and Construct interaction networks with a well-defined set of actors with a presumed role in a given context.

This section provides an overview on any TF, gene or miRNA, including their interactions: The "Quick Search" is a full text search engine which provides knowledge for single candidates, while the "Quick Network" is a powerful application to construct networks from a given list of TFs, miRNAs and other genes with a presumed function within a biological context, as supported by literature or experimental data.

Identify novel major regulators and Detect sub-networks through the construction and analysis of networks.

This query includes three sections: "Transcription Factor regulation" determines potential TF⇒miRNA regulations from a list of TFs or miRNAs; "miRNA regulation" determines potential miRNA⇒Gene regulations from a list of miRNAs or genes and; "Regulation Network" allows meta-regulation network construction, including network motif detection.

MIR@NT@N help - A contextual guide to assist the user

MIR@NT@N help main page includes an overall description of each section, including a quick tutorial and example files (see below). To guide users in their analysis, MIR@NT@N also provides a contextual help available within each section, by explaining parameters, checking loaded data, and suggesting analysis refinement.

MIR@NT@N is able to deal with lists of miRNA, TF and/or gene. Here are example files used in MIR@NT@N article:
miRNA list: cluster of 3 members of the miRNA 200 family, known to be down-regulated in the EMT ('Epithelium to Mesenchyme Transition').
TF list: list of 4 transcription fators found to be major regulators of the miRNA 200 family (previous miRNA list) with MIR@NT@N.
Gene list: list of 132 genes found to be up-regulated in 'Epithelium to Mesenchyme Transition' (Vetter and Le Béchec et al., 2009).
Combined list: members of miRNA 20 family, TF found and target gene (use with "Quick Network Generation" section).
Load these example files as “Tab-delimiter File format” with M@GIE module.

MIR@NT@N database

Database dump [~200Mo]
Zip file (SQL format) of the database (release 03/12/2010)

TFBS on miRNA upstream sequence [~20Mo]
Zip file (tab-del) with TFBS scores calculated from miRNA upstream sequence

Meta-regulation network [~4Mo]
Zip file (tab-del) of all regulations (TF⇒miRNA, miRNA⇒Gene, TF⇒Gene) for a common standard score threshold of 0.85

Motif Scoring Procedure and Computation of JASPAR Profile Matrix Score p-values
To allow researchers to better interpret the thresholds, this web page describes the motif scoring procedure (from Fickett, 1996), and indicates the correspondence of the scores with empirically derived p-values (for a common reference DNA sequence).

Based on M@IA environment - Datamining module

Based on a flexible modular approach, the M@IA environment offers an interactive multi-user interface which includes all steps of a microarray study: from MIAME-compliant storage of experiments and raw data processing to analysis of differentially regulated genes. In addition, M@IA offers functional insight into gene expression data by using an original integrative biology approach combining biological knowledge annotation with gene expression data through interactive graph.
M@IA development Team M@IA environment Website

About MIR@NT@N contributors

MIR@NT@N team contact