microRNA databases and research software

I. microRNA databases

1.miRBase

http://www.mirbase.org/

miRBase This sequence database provides published miRNA sequences, annotations and predicted gene targets and is a major public repository for miRNA information. miRBase offers online searches for known miRNAs and targets by keyword or sequence. The original article locates miRBase at the University of Manchester and identifies support from UK research councils and the Wellcome Sanger Institute.

2.miRecords

http://mirecords.biolead.org/

A database of animal miRNA–target interactions, including manually collected experimentally validated and predicted targets. Prediction tools listed include DIANA-microT, MicroInspector, miRanda, MirTarget2, miTarget, NBmiRTar, PicTar, PITA, RNA22, RNAhybrid and TargetScan/TargetScanS. University of Minnesota, USA.

3.PMRD

http://bioinformatics.cau.edu.cn/PMRD/

PMRD A plant microRNA database covering sequences, target genes, secondary structures, expression profiles and genomic searches, with the aim of integrating plant microRNA data. China Agricultural University, Beijing, China.

4.CoGeMiR

http://cogemir.tigem.it/

CoGeMiR This database summarizes evolutionary conservation of microRNAs across animals and collects chromosome locations, conservation and expression profiles for known and predicted microRNAs. Telethon Institute of Genetics and Medicine, Italy.

5.miRWalk

http://www.ma.uni-heidelberg.de/apps/zmf/mirwalk/

miRWalkis An integrated database of predicted miRNAs and validated binding sites in their target genes for humans, mice and rats. Heidelberg University, Germany.

6.TarBase

http://diana.cslab.ece.ntua.gr/tarbase/

TarBase A manually curated database of experimentally validated miRNA targets in humans, mice, fruit flies, worms and zebrafish, distinguishing supported and unsupported target interactions. Institute of Molecular Oncology, Varkiza, Greece.

7.miRGator:http://genome.ewha.ac.kr/miRGator/miRGator.html

miRGator A tool for interpreting miRNA function. Functional analysis and expression profiles can be combined with predicted targets to explore possible biological functions. Ewha Womans University, Seoul, South Korea.

8.miRGen

http://www.diana.pcbi.upenn.edu/miRGen.html

miRGen An integrated database of positional relationships between animal miRNAs and genomic elements, together with predicted animal miRNA targets from widely used prediction programs. University of Pennsylvania, USA.

9.miRNAMap

http://mirnamap.mbc.nctu.edu.tw/

miRNAMap A collection of experimentally supported microRNAs and miRNA targets across species, including human, mouse, rat and other multicellular animal genomes. Institute of Bioinformatics, National Chiao Tung University, Hsinchu, Taiwan.

10.Vir-Mir

http://alk.ibms.sinica.edu.tw/cgi-bin/miRNA/miRNA.cgi

Vir-Mir A database of candidate hairpin sequences predicted for viral miRNAs. Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan.

11.ViTa

http://vita.mbc.nctu.edu.tw/

ViTa A viral database integrating resources including miRBase, ICTV, VirGne and VBRC, covering known viral miRNAs and host targets predicted by miRanda and TargetScan. ViTa also provides annotations such as human miRNA expression and infected tissues. Institute of Bioinformatics, National Chiao Tung University, Hsinchu, Taiwan.

12.ASRP Database

http://asrp.danforthcenter.org/

ASRP A resource for Arabidopsis small RNAs isolated by ASRP or other laboratories. Oregon State University, USA.

13.miRNApath

http://lgmb.fmrp.usp.br/mirnapath/tools.php

miRNApath A database of miRNAs, target genes and metabolic pathways. Department of Genetics, University of São Paulo, Brazil.

14.miRex

http://miracle.igib.res.in/mirex/

miRex An online resource collecting, curating and analyzing published microRNA expression data. It lets researchers examine expression across thousands of data points and store microRNA expression data online. Institute of Genomics and Integrative Biology, India.

15.PolymiRTS

http://compbio.uthsc.edu/miRSNP/

A database of naturally occurring DNA variants in miRNA target sites. University of Tennessee Health Science Center, USA.

II. microRNA research software

1.SeqBuster

http://seqcluster.readthedocs.org/mirna_annotation.html

a bioinformatic web interface able to custom analyze deep sequencing data to study miRNA variants or isomiRs. From Genetic Causes of Disease Group, Genes and Disease Program, Centre for Genomic Regulation (CRG), Pompeu Fabra University, Barcelona, Catalonia, Spain.

2.WMD3

http://wmd3.weigelworld.org./cgi-bin/webapp.cgi?

WMD3 designs artificial microRNAs (amiRNAs). The 21mer amiRNA21mers can specifically silenceg single or multiple genes of interest in more than 90 plants. From Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany.

3.TargetScan

http://www.targetscan.org/

TargetScan Predicts target genes by searching for conserved 8-mer and 7-mer sites matching each miRNA seed region. Whitehead Institute for Biomedical Research, USA.

4.microRNA.org

http://www.microrna.org/

miRanda Provides predicted microRNA targets and tissue expression profiles for human, fruit-fly and zebrafish genomes. Memorial Sloan Kettering Cancer Center, USA.

5.PicTar

http://www.pictar.org/

PicTar Uses computational rules to identify microRNA targets. The searchable resource covers vertebrates, seven fruit-fly species, three nematode species and nonconserved but co-expressed human microRNA targets, such as miRNAs and mRNAs expressed in the same tissue. Max Delbrück Center, Berlin, and the Rajewsky laboratory, New York University.

6.RNAhybrid

http://bibiserv.techfak.uni-bielefeld.de/rnahybrid/

RNAhybrid A tool for finding minimum-free-energy pairing between a long RNA and a short RNA, including favorable binding positions; it is used for microRNA target prediction. Bielefeld University, Germany.

7.microInspector

http://bioinfo.uni-plovdiv.bg/microinspector/

microInspector Provides miRNA binding-site predictions. Institute of Molecular Biology and Biotechnology, Heraklion, Greece, and Plovdiv University, Bulgaria.

8.TripletSVM

http://bioinfo.au.tsinghua.edu.cn/mirnasvm/

TripletSVM A program that predicts whether a queried hairpin sequence is a genuine miRNA precursor. Tsinghua University, Beijing, China.

III. microRNA function and mechanism resources

TransmiR

http://cmbi.bjmu.edu.cn/transmir

TransmiR A database of microRNA regulation of transcription factors, described as free for academic laboratories. Peking University, Beijing, China.

miR2Disease

http://www.mir2disease.org/

miR2Disease A manually curated database of microRNAs associated with human diseases. Harbin Institute of Technology, China.

S-MED

http://www.oncomir.umn.edu/SMED/index.php

S-MED The sarcoma microRNA expression database stores miRNA expression profiles from multiple human sarcomas and selected normal tissues. University of Minnesota, USA.

IV. microRNA target-prediction links