miRNet
- a miRNA-centric network visual analytics platform
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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
Please reach us via our
OmicsForum
to ask questions related to miRNet.
We are testing our
OmicsBot
(bottom-right of each page) for better analysis support.
Check out our new book chapter on
MicroRNA Regulatory Network Analysis Using miRNet 2.0
(
11/08/2022
);
Upgraded to Primefaces 12.0.0 (
10/12/2022
);
Added the FDR column to the download table of enrichment analysis result (
08/02/2022
);
Upgraded R to version 4.1.3 and code refactoring (
05/13/2022
);
For miRNetR users, the path to sqlite database is: https://www.xialab.ca/resources/
sqlite
/mir2gene.sqlite (
02/24/2022
);
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
Chang, L. and Xia, J. (2022)
MicroRNA Regulatory Network Analysis Using miRNet 2.0
Transcription Factor Regulatory Networks, 185-204. Humana Press, New York, NY
Chang, L., Zhou, G., Soufan, O. and Xia, J. (2020)
miRNet 2.0 - network-based visual analytics for miRNA functional analysis and systems biology
.
Nucl. Acids Res. (doi: 10.1093/nar/gkaa467)
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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