miRNet
-- an integrated platform linking miRNAs, targets & functions
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About
Support
miRNA input
gene input
other input
xeno-miRNAs
Transcription factors
RT-qPCR data
lncRNAs
miRNA list
Small molecules
Gene list
Expression table
Epigenetic modifiers
RNAseq raw reads
Diseases
Xeno-miR browser
Xeno-miR search
News & Updates
Added a new module to support miRNA and transcription factor interactions (
12/03/2019
);
Updated miRNA-disease interaction data based on new release of HMDD v3.2 (
11/08/2019
);
Updated R from 3.5.1 to the latest version (3.6.1) (
10/16/2019
);
Added support for pig (429 miRNAs and 8353 target genes) (
10/09/2019
);
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
);
Read more ......
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
twelve
different miRNA databases -
TarBase
,
miRTarBase
,
miRecords
,
miRanda
(
S mansoni
only),
miR2Disease
,
HMDD
,
PhenomiR
,
SM2miR
,
PharmacomiR
,
EpimiR
,
starBase
, and
TransmiR
. 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.
High-performance network visual analytics
: miRNet offers six types of networks on
miRNA-gene
,
miRNA-disease
,
miRNA-small molecule
,
miRNA-lncRNA
,
miRNA-epigenetic modifier
, and
miRNA-transcription factor
. 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
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