Input Type
Click on a module below to start
Mixed input types
Multiple query types
Upload a data table
Expression table
RT-qPCR data
Select from a database
Diseases
Small compounds
Epigenetic modifiers
Xeno-miR explorer
Upload a query list
miRNAs
SNPs
Genes
ncRNAs
Transcription factors
Xeno-miRs
News & Updates
  • Upgraded to Primefaces 10 (03/30/2021);
  • Enhanced support for PNG export - up to 3X larger (01/29/2021);
  • Fixed the issue with network export (01/29/2021);
  • Fixed the issue with tissue mapping in gene, TF and ncRNA modules (01/28/2021);
  • Fixed the issue with empirical sampling when microservice failed (12/22/2020);
  • Fixed the issue with Steiner Forest algorithm (11/24/2020);
  • Check out our video tutorials for intuitive network visual analytics (10/15/2020);
  • Updated R from 3.6.2 to 4.0.2 and code refactoring (09/15/2020);
  • Added support for gradient background (09/14/2020);
  • Added support to show piechart nodes with multiple annotations (i.e. lncRNA and Gene, TF and Gene) (07/30/2020);
  • Users can now select the original database for miRNA gene target analysis (07/06/2020)
Read more ......
Key Features
  • Support for various inputs & statistics: miRNet accepts a list of miRNAs, miR-SNPs, genes, transcription factors, small molecules, ncRNAs, diseases, epigenetic modifers, any of their combinations 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 14 different miRNA databases - TarBase, miRTarBase, miRecords, miRanda (S mansoni only), miR2Disease, HMDD, PhenomiR, SM2miR, PharmacomiR, EpimiR, starBase, TransmiR, ADmiRE, and TAM 2.0. It currently supports Human, Mouse, Rat, Cattle, Pig, 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. The network algorithm includes Force Atlas, Fruchterman-Reingold, Graphopt, Large Graph, Random, Reduce Overlap, Bipartite/Tripartite, Concentric Circle, and Backbone algorithm.
  • High-performance network visual analytics: miRNet allows users to easily create miRNA-centric networks consisting of different molecules or phenotypes of interest: genes, diseases, small molecules, SNPs (affecting miRNAs or their binding sites), ncRNAs (lncRNA, sncRNA, circRNA or peudogene), epigenetic modifiers, and transcription factors. The system supports zooming, batch highlighting, point-and-click, drag-and-drop, enrichment analysis, etc. to enable users to intuitively explore miRNAs, targets and functions.
Publications
Acknowledgements
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