alexa MIR@NT@N: a framework integrating transcription factors, microRNAs and their targets to identify sub-network motifs in a meta-regulation network model.
Genetics & Molecular Biology

Genetics & Molecular Biology

Journal of Tissue Science & Engineering

Author(s): Le Bchec A, PortalesCasamar E, Vetter G, Moes M, Zindy PJ,

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Abstract BACKGROUND: To understand biological processes and diseases, it is crucial to unravel the concerted interplay of transcription factors (TFs), microRNAs (miRNAs) and their targets within regulatory networks and fundamental sub-networks. An integrative computational resource generating a comprehensive view of these regulatory molecular interactions at a genome-wide scale would be of great interest to biologists, but is not available to date. RESULTS: To identify and analyze molecular interaction networks, we developed [email protected]@N, an integrative approach based on a meta-regulation network model and a large-scale database. [email protected]@N uses a graph-based approach to predict novel molecular actors across multiple regulatory processes (i.e. TFs acting on protein-coding or miRNA genes, or miRNAs acting on messenger RNAs). Exploiting these predictions, the user can generate networks and further analyze them to identify sub-networks, including motifs such as feedback and feedforward loops (FBL and FFL). In addition, networks can be built from lists of molecular actors with an a priori role in a given biological process to predict novel and unanticipated interactions. Analyses can be contextualized and filtered by integrating additional information such as microarray expression data. All results, including generated graphs, can be visualized, saved and exported into various formats. [email protected]@N performances have been evaluated using published data and then applied to the regulatory program underlying epithelium to mesenchyme transition (EMT), an evolutionary-conserved process which is implicated in embryonic development and disease. CONCLUSIONS: [email protected]@N is an effective computational approach to identify novel molecular regulations and to predict gene regulatory networks and sub-networks including conserved motifs within a given biological context. Taking advantage of the [email protected] environment, [email protected]@N is a user-friendly web resource freely available at http://mironton.uni.lu which will be updated on a regular basis.
This article was published in BMC Bioinformatics and referenced in Journal of Tissue Science & Engineering

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