RNA-Seq Blog Transcriptome Research & Industry News
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 | http://202.38.126.151/hmdd/mirna/md |
| PhenomiR | Database of miRNA related phenotypes | http://mips.helmholtz-muenchen.de/phenomir |
| miRenvironment | Database of validated miRNA–environment interactions | http://202.38.126.151/hmdd/tools/miren.html |
| 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]
