Table 5.
miRNA databases.
| Name | Link | Description | Organism | PMID |
|---|---|---|---|---|
| ChIPBase v2.0 | http://rna.sysu.edu.cn/chipbase/ | regulatory networks of ncRNAs and protein-coding genes | human | 27924033 |
| deepBase v2.0 | http://biocenter.sysu.edu.cn/deepBase/ | small RNAs, LncRNAs and circular RNAs | 19 species | 26590255 |
| DIANA-TarBase v7.0 | http://www.microrna.gr/tarbase | experimentally validated miRNA:gene interactions | 24 species | 25416803 |
| doRiNA v2.0 | http://dorina.mdc-berlin.de/ | RNA interactions in post-transcriptional regulation | human, mouse, fly and worm | 25416797 |
| dPORE | http://cbrc.kaust.edu.sa/dpore | SNPs on the regulation of miRNAs and predicted TFBSs | human | 21326606 |
| Firefly Discovery Engine | https://www.fireflybio.com/portal/search | published miRNA papers | 6 species | NA |
| HOCTAR2 | http://hoctar.tigem.it/ | miRNA target and expression | human | 21435384 |
| mESAdb | http://konulab.fen.bilkent.edu.tr/mirna/ | sequences and expression of miRNA | human, mouse and zebrafish | 21177657 |
| microRNA.org | http://www.microrna.org | targets and expression | human, mouse, rat, fly and worm | 18158296 |
| miRBase | http://www.mirbase.org/ | miRNA sequences and annotation | 206 species | 24275495 |
| miRCancer | http://mircancer.ecu.edu/ | miRNA Cancer Association | human | 23325619 |
| miRDB | http://www.mirdb.org/ | targets and functional annotations | human, mouse, rat, dog and chicken | 25378301 |
| miRecords | http://miRecords.umn.edu/miRecords | animal miRNA-target interactions | 9 species | 18996891 |
| miRGate | http://mirgate.bioinfo.cnio.es | miRNA-mRNA targets | human, mouse and rat | 25858286 |
| miRGator v3.0 | http://mirgator.kobic.re.kr/ | expression profiles and target relationships | human | 23193297 |
| miRGen v2.0 | http://www.microrna.gr/mirgen | cell-line-specific miRNA TSSs and TF binding sites | human and mouse | 26586797 |
| miRmine | http://guanlab.ccmb.med.umich.edu/mirmine | miRNA expression profiles | human | 28108447 |
| miRNAMap v2.0 | http://miRNAMap.mbc.nctu.edu.tw/ | experimentally verified microRNAs and miRNA target genes | human, mouse, rat and other metazoan genomes | 18029362 |
| miRNEST v2.0 | http://mirnest.amu.edu.pl | collection of animal, plant and virus microRNA data | 544 species | 24243848 |
| miROrtho | http://cegg.unige.ch/mirortho | miRNA gene candidates | 45 species | 18927110 |
| miRSel | http://services.bio.ifi.lmu.de/mirsel | literature derived miRNA-gene association | human, mouse and rat | 20233441 |
| miRTarBase v7.0 | http://miRTarBase.mbc.nctu.edu.tw/ | experimentally validated miRNA-target interactions | 23 species | 29126174 |
| miRWalk v2.0 | http://zmf.umm.uni-heidelberg.de/mirwalk2 | predicted and experimentally verified miRNA-target interactions | 15 species | 26226356 |
| PMRD | http://bioinformatics.cau.edu.cn/PMRD | plant microRNA | 21 plant species | 19808935 |
| PolymiRTS Database | http://compbio.uthsc.edu/miRSNP/ | DNA variations in miRNA seed regions and miRNA target sites | human and mouse | 24163105 |
| Psmir | http://www.bio-bigdata.com/Psmir/ | potential associations between small molecules and miRNAs | human | 26759061 |
| RepTar | http://reptar.ekmd.huji.ac.il | predicted miRNA target | human and mouse | 21149264 |
| SonamiR DB v2.0 | http://compbio.uthsc.edu/SomamiR/ | cancer somatic mutations in miRNAs and their target sites | human | 26578591 |
| StarBase v2.0 | http://starbase.sysu.edu.cn/ | RNA-RNA and protein-RNA interaction networks from CLIP-Seq data | human, mouse and worm | 24297251 |
| STarMirDB | http://sfold.wadsworth.org/starmirDB.php | miRNA binding sites | human, mouse and worm | 27144897 |
| TargetScan v7.1 | http://www.targetscan.org/vert_71/ | miRNA targets | human, mouse, worm, fly and fish | 26267216 |
| TMREC | http://bioinfo.hrbmu.edu.cn/TMREC/ | transcription factor and miRNA regulatory cascades in human diseases | human | 25932650 |
| TransmiR | http://cmbi.bjmu.edu.cn/transmir | transcription factor–microRNA regulation | 14 species | 19786497 |
| VIRmiRNA | http://crdd.osdd.net/servers/virmirna | experimental viral miRNA and their targets | 68 viruses | 25380780 |