miRNet

-- an integrated platform linking miRNAs, targets & functions

Welcome to miRNet

Each circle corresponds to a specific type of input. Click a circle on the right to proceed.

miRNet is a user-friendly, integrated tool suite designed for comprehensive analysis and functional interpretation of miRNAs and xeno-miRNAs. To achieve this goal, miRNet leverages multiple high-quality knowledgebase to connect miRNAs to their targets, other associated molecules as well as phenotypes (i.e. diseases). The information is presented through a powerful network visual analytics system to allow intuitive exploratory data analysis. Different functional enrichment analysis can be performed in situ to facilitate hypothesis generation.

News & Updates

Minor code refactoring for better performance (06/06/2019);
Upgraded the web framework to PrimeFaces 7.0 (05/29/2019);
Fixed the issue with file uploading (03/11/2019);
Fixed the bugs in tissue mapping (03/07/2019);
Added two modules to support analysis of xeno-miRNAs (xenomiRs) and their potential targets in different hosts (02/25/2019);
Updated the interface for improved performance and better user experience (02/20/2019);
A detailed protocol on using miRNet is now available (11/20/2018);
Updated the framework for better performance (08/19/2018);
Added exosomal miRNA annotation for human miRNAs (01/05/2018);

Key Features

Support for various inputs & statistics: miRNet accepts a list of miRNAs or targets, or a data table from microarray, RNAseq or RT-qPCR experiments. miRNet supports differential analysis using limma, edgeR and HTqPCR methods; enrichment analysis using standard hypergeometric tests and unbiased random sampling.
Comprehensive functional annotation: miRNet integrates data from eleven different miRNA databases - TarBase, miRTarBase, miRecords, miRanda (S mansoni only), miR2Disease, HMDD, PhenomiR, SM2miR, PharmacomiR, EpimiR, and starBase. It currently supports Human, Mouse, Rat, Cattle, Chicken, Zebra fish, Fruit fly, C. elegans and S. mansoni.
Exploring xeno-miRNAs and their potential targets: miRNet currently supports six hosts (Human, Mouse, Chicken, Fruit fly, and C. elegans) with xeno-miRNAs reported from over 50 species. It contains over 400 experimentally detected xeno-miRNAs supplemented with 1000 computational predicted transportable miRNAs. Their potential gene targets are predicted using two algorithms - miRanda and TarPmiR.
Creation of miRNA-target interaction networks: miRNet provides a wide array of options to allow researchers to build miRNA-target interaction networks at different confidence levels. The resulting network can be further optimized using different algorithms to improve visualization and understanding.
High-performance network visual analytics: miRNet offers five types of networks on miRNA-gene, miRNA-disease, miRNA-small molecule, miRNA-lncRNA, and miRNA-epigenetic modifier. The system supports zooming, highlighting, point-and-click, drag-and-drop, enrichment analysis, etc. to enable users to intuitively explore miRNAs, targets and functions.

Publications

Fan, Y., Habib, M. and Xia, J. (2018) Xeno-miRNet: a comprehensive database and analytics platform to explore xeno-miRNAs and their potential targets PeerJ 6:e5650
Fan Y. and Xia, J. (2018) miRNet: functional analysis and visual exploration of miRNA-target interactions in a network context Computational Cell Biology. Humana Press, New York, NY
Fan Y, Siklenka, K., Arora, SK., Ribeiro, P., Kimmins, S. and Xia, J. (2016) miRNet - dissecting miRNA-target interactions and functional associations through network-based visual analysis. Nucl. Acids Res. 44 W135–141

Acknowledgements