Web Tools for miRNA Analysis

An overview of databases and repositories of miRNA sequences and expression, a commentary on miRNA target prediction algorithms, tools for miRNA functional investigation, and online pipelines for the analysis of high throughput experiments. Examples and case studies are provided at the end of the manuscript, which can hopefully contribute in elucidating the utility of these implementations to basic and applied research.

Only tools offering a fully functional web interface have been included, excluding implementations requiring deployment in local servers or workstations.

Selected online resources (sorted by type and order of presentation within the manuscript).

Application name Type Web address
miRBase miRNA sequence and annotation archive http://www.mirbase.org
smirnaDB miRNA expression database http://www.mirz.unibas.ch/cloningprofiles
microRNA.org — miRNA Expression miRNA expression database http://www.microrna.org/microrna/getExprForm.do
miRNEYE miRNA expression database http://mirneye.tigem.it
S-MED//CC-MED miRNA expression database http://www.oncomir.umn.edu/SMED & http://www.oncomir.umn.edu/colon/basic_search.php
TargetScan miRNA target prediction http://www.targetscan.org
DIANA-microT-CDS miRNA target prediction http://www.microrna.gr/microT-CDS
microRNA.org miRNA target prediction http://microrna.org
miRDB miRNA target prediction http://www.mirdb.org
RNA22 miRNA target prediction http://cm.jefferson.edu/rna22v1.0-homo_sapiens
TargetMiner miRNA target prediction http://www.isical.ac.in/~bioinfo_miu/targetminer20.htm
PicTar miRNA target prediction (http://pictar.mdc-berlin.de)
DIANA-TarBase Manually curated validated mirna target database http://www.microrna.gr/tarbase
miRTarBase Manually curated validated mirna target database http://mirtarbase.mbc.nctu.edu.tw
miRecords Manually curated validated mirna target database http://mirecords.biolead.org
StarBase Sequence based miRNA experiment database http://starbase.sysu.edu.cn
DIANA-miRPath miRNA pathway analysis http://www.microrna.gr/miRPathv2
miTalos miRNA signaling pathway analysis http://mips.helmholtz-muenchen.de/mitalos
GeneTrail Gene set analysis tool http://genetrail.bioinf.uni-sb.de
miRGator Integrated system for functional investigation of miRNAs http://mirgator.kobic.re.kr
miR2Disease Database of miRNA related diseases http://www.mir2disease.org
HMDD Database of miRNA related diseases
PhenomiR Database of miRNA related phenotypes http://mips.helmholtz-muenchen.de/phenomir
miRenvironment Database of validated miRNA–environment interactions
wapRNA RNA-Seq analysis http://waprna.big.ac.cn
DSAP RNA-Seq analysis http://dsap.cgu.edu.tw
miRanalyzer RNA-Seq analysis http://bioinfo2.ugr.es/miRanalyzer/miRanalyzer.php
miRCat RNA-Seq analysis http://srna-tools.cmp.uea.ac.uk/animal/cgi-bin/srna-tools.cgi?rm=input_form&tool=mircat


Vlachos IS, Hatzigeorgiou AG. (2014) Online resources for miRNA analysis. Clin Biochem 46(10-11), 879-900. [abstract]