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. 2015 Nov 17;44(1):24–44. doi: 10.1093/nar/gkv1221

Table 3. Bioinformatic resources to deal with different aspects of microRNA related research.

Category Tools Type Organism(s) Input data MRV LU URL References
Finding validated miRNA information DIANA-TarBase Database h,m,r,f,w,z + 18 more MI 21 2015Y http://www.microrna.gr/tarbase (113,114)
miRTarBase Database h,m,r,f,w,z + 12 more MI, MF, GS,KP,VM, DN,PIMD, ML,GL 20 2013Y http://mirtarbase.mbc.nctu.edu.tw (115,116)
miRecords Database h,m,r,f,w,z,cn,sh MI,GI 11,20 2013Y http://c1.accurascience.com/miRecords/ (117)
StarBase Database h,m,w + 3 more MI,GS 15, 20 2014Y http://starbase.sysu.edu.cn/ (118,119)
Correlating miRNA and mRNA expression MiRonTop Database - 15 2010N http://www.microarray.fr:8080/miRonTop/index (120)
DIANA-mirExTra Web server h,m GL 10 2010N http://diana.cslab.ece.ntua.gr/hexamers/ (121)
mESAdb Database h,m,z MI.ML 15 2010N http://konulab.fen.bilkent.edu.tr/mirna/mESAdb_information.php (123)
miRGator Database h MI, 18 2013Y http://mirgator.kobic.re.kr/index.html (127)
miRNA regulatory network identification MAGIA Web server h ML, GI, GED,MED 14 2009N http://gencomp.bio.unipd.it/magia/start/ (128)
mirConnX Web server h, m GED,MED 14 2011Y http://www.benoslab.pitt.edu/mirconnx (130)
CoMeTa Database h GB,KP,MI 13 2012Y http://cometa.tigem.it/ (131)
miRNA metabolic and signaling pathway analysis ElMMo Web server h,m,r,w,f,z MRI, MRL, MI 11 2009N http://www.mirz.unibas.ch/ElMMo/ (135)
miRNApath Database h,m,r,d GL,MI 9.2 2007N http://lgmb.fmrp.usp.br/mirnapath (136)
miTALOS Web server h, m MI, MC,TT, KP, NP - 2011Y http://hmgu.de/cmb/mitalos (137)
miRSystem Database h, m ML, PD, GS 20 2015Y http://mirsystem.cgm.ntu.edu.tw/ (138)
DIANA-miRPath Web server h, m, r, f,w,z cn, MI 18, 21 2015Y http://snf-515788.vm.okeanos.grnet.gr/dianauniverse/index.php?r=mirpath (122,139,140)
miRNA and transcription factor interaction TransmiR Database h,m,r,w + 12 more TF, MI - 2013Y http://cmbi.bjmu.edu.cn/transmir (142)
PuTmiR Database h MI 14 2010N http://www.isical.ac.in/∼bioinfo_miu/TF-miRNA/TF-miRNA.html (143)
CircuitsDB Database h,m TF, MI,GS 9.2 2010N http://biocluster.di.unito.it/circuits/index.php (144)
MIR@NT@N Software paper 14 2010N http://maia.uni.lu/mironton.php (145)
ChIPBase Database h,m,d,cn,f,w TF, MI, RR 17 2012Y http://deepbase.sysu.edu.cn/chipbase/ (146)
miRNA deregulation in human disease miR2Disease Database h MI,DN,TG 11 2008N http://www.mir2disease.org/ (151)
miRò Database h,m MI,GS, DN,P,T 12 2009N http://ferrolab.dmi.unict.it/miro/ (152)
PhenomiR Database h MI,DN,PI, T/C,SD,M,TG 12 2011Y http://mips.helmholtz-muenchen.de/phenomir/ (153)
OncomiRDB Database h MI, TT, T, TG,F 16,20 2014Y http://bioinfo.au.tsinghua.edu.cn/member/jgu/oncomirdb/index.php (154)
miRCancer Database h MI, Cancer name 18 2015Y http://mircan-cer.ecu.edu/ (155)
HMDD Database h MI,DN 20 2014Y http://210.73.221.6/hmdd (156)
Extracellular circulating miRNA miRandola Database h MI,MF,MT,D, S,PB 18 2015Y http://atlas.dmi.unict.it/mirandola/index.html (158)
Linking miRNA, environmental factors and phenotype miREnvironment Database h, m, r, d, cn, c, cw, fr, z, p w MI, EF,P,S 17 2012Y http://210.73.221.6/miren (165)
Linking polymorphisms in miRNA target with human disease Patrocles database h,m,r,c,cn,d,cw - 11 2009N http://www.patrocles.org/ (171)
MicroSNiPer h,m US,GI,SI 15,19 2012Y http://epicenter.ie-freiburg.mpg.de/services/microsniper/ (172)
Mirsnpscore Database h GI,MI,SI 16 2010N http://www.bigr.medisin.ntnu.no/mirsnpscore/ (174)
MirSNP Database h GN, R,SI,MI, GL, MRL,SL 18 2012Y http://202.38.126.151/hmdd/mirsnp/search/ (175)
miRdSNP Database h GN,MI, PM,SI,D,DS 18 2011Y http://mirdsnp.ccr.buffalo.edu/ (170)
PolymiRTS Database h,m SI,MI,GI,GD, T,GO 17,20 2013Y http://compbio.uthsc.edu/miRSNP/ (176,177)
Somatic mutations in miRNAs and their target sites SomamiR Database h CL, MI, GI, GS 17 2012Y http://compbio.uthsc.edu/SomamiR/ (179)
miR2GO Web server h MSE, MI, SI, MP 21 2015Y http://compbio.uthsc.edu/miR2GO/home.php (180)
Prediction of cellular target of host and viral miRNA ViTa Database H,m,r,cn VI,MI,D,IT 8.2 2006N http://vita.mbc.nctu.edu.tw/ (181)
Vir-Mir db Database h,m,r,z GB,RA, VN 9 2007N http://alk.ibms.sinica.edu.tw/ (56)
Bi-Targeting Method h - 14 2010N http://www.cs.bgu.ac.il/∼vaksler/BiTargeting.htm (182)
RepTar Database h, m MS, MI, GN 15 2010N http://reptar.ekmd.huji.ac.il/ (183)

Input data: KP, KEGG pathway; VM, validated method; DN, disease name; ML, miRNA list; GL, gene list; GS, Gene symbol; RR, regulatory region;,DN, disease name; TG, target gene, TT, tissue type; T, tumor; F, function; EF, environmental factor; P, phenotype; S, species, US, 3′ UTR sequence; SI,SNP ID; MS, miRNA seed, GN, gene name; MR, mRNA ID; MI, miRNA ID; GL, gene list; MRL, mRNA list; SL, SNP list; DS, distance between SNP and miRNA target site in nucleotides, GD, gene description; T, trait; GA, GO accession; CL, Chromosome Location, VI, virus ID; IT, infected tissue of virus; GB, GenBank Id of virus; RA, RefSeq accession of virus; VN, viral scientific name; MS, miRNA source; GED, gene expression data; MED, miRNA expression data; GB, GO term Biological Process FAT; MRI, mRNA ID; MC, miRNA cluster; NP, NCI pathway; PD, pathway database; MSE, miRNA sequence; MP, miRNA pair

Organisms: h, human; m, mouse; r, rat; d, dog; cn, chicken; c, chimpanzee; cw, cow; fr, frog; z, zebrafish; f, fly; w, worm; p, pig; sh, sheep

MRV: miRBase release version

LU, last updated: Yupdated over the past 5 years, Nnot updated.