microRNA | microRNA web resources
Mary Johnson (mary at labome dot com)
Synatom Research, Princeton, New Jersey, United States
DOI
http://dx.doi.org/10.13070/mm.en.2.131
Date
last modified : 2015-02-17; original version : 2012-10-20
Cite as
MATER METHODS 2012;2:131
Abstract

A central web resource for microRNA research, including microRNA databases, microRNA prediction and microRNA target prediction tools, microRNA expression profiling, functions

microRNA databases
miRBase

miRBase (www.mirbase.org) provides published miRNA sequences, annotations, predictions for target, etc. and a convenient online enquiry interface, allowing users to search known miRNA and target information through keywords or sequences [1]. It is one of the main microRNA sequence databases. miRBase is hosted and maintained in University of Manchester, Faculty of Life Sciences, United Kingdom, funded by BBSRC, and by the Wellcome Trust Sanger Institute (previously).

As of February, 2015, the current version is 21 (released in June 2014). This version contains 28645 entries representing hairpin precursor miRNAs expressing 35828 mature miRNA products, in 223 species. The database is actively maintained and is being updated continuously.

miRBase is one of the expert databases participating in RNAcentral [2].

PMRD/PNRD. PMRD: plant microRNA database. The updated version in November 2014 is called PNRD (Plant Non-coding RNA Database).

PMRD (bioinformatics.cau.edu.cn/PMRD/) is a microRNA database focused on plant species. It consists of microRNA sequences and their target genes, secondary dimension structure, expression profiling, genome browser, etc. and attempts to integrate the large amount of information of plant microRNAs data [3]. As of Oct 20, 2012, it includes over 130 plant species including rice, tomato, cotton, soybean, peanut, and Arabidopsis thaliana. From China Agricultural University, Beijing, China.

The updated version in November 2014 is called PNRD (Plant Non-coding RNA Database) [4], extending to cover not only miRNAs, but also other non-coding RNAs. It contains 25739 entries of 11 types of ncRNAs from 150 plant species, with 1581 miRNA, 2579 lncRNA, 23 tasiRNA, and 1432 others from Arabidopsis thaliana, 2819 miRNA, 752 lncRNA, 9 tasiRNA, and 1313 others from Oryza sativa, and 2944 miRNA and 538 lncRNA from Populus trichocarpa [4].

miRWalk 2.0: microRNA target database

miRWalk (www.ma.uni-heidelberg.de/apps/zmf/mirwalk/) is a comprehensive database that provides information on miRNA from human, mouse and rat on their predicted as well as validated and predicted binding sites on their target genes [5, 6]. From Ruprecht-Karls-Universität Heidelberg, Medizinische Fakultät Mannheim, Germany.

The validated target module is last updated in September, 2014. based on more than 7000 publications, has information on 2044 miRNAs from human, mouse, and rat, more than 67598 relationship associated to 3821 genes, 375 pathways, 549 diseases, 468 organs, 74 cell lines and 2033 OMIM disorders.

The predicted database is built with 12 microRNA target prediction softwares: DIANA-microTv4.0, DIANA-microT-CDS, miRanda-rel2010, mirBridge, miRDB4.0, miRmap, miRNAMap, doRiNA, PicTar2, PITA, RNA22v2, RNAhybrid2.1 and Targetscan6.2. This module is based on miRBase release 20.

doRiNA 2.0

dorina.mdc-berlin.de is a database of RNA interactions in post-transcriptional regulation [7, 8]. "In animals, RNA binding proteins (RBPs) and microRNAs (miRNAs) post-transcriptionally regulate the expression of virtually all genes by binding to RNA. Recent advances in experimental and computational methods facilitate transcriptome-wide mapping of these interactions. It is thought that the combinatorial action of RBPs and miRNAs on target mRNAs form a post-transcriptional regulatory code. We provide a database that supports the quest for deciphering this regulatory code. Within doRiNA, we are systematically curating, storing and integrating binding site data for RBPs and miRNAs. Users are free to take a target (mRNA) or regulator (RBP and/or miRNA) centric view on the data. We have implemented a database framework with short query response times for complex searches (e.g. asking for all targets of a particular combination of regulators). All search results can be browsed, inspected and analyzed in conjunction with a huge selection of other genome-wide data, because our database is directly linked to a local copy of the UCSC genome browser. At the time of writing, doRiNA encompasses RBP data for the human, mouse and worm genomes. For computational miRNA target site predictions, we provide an update of PicTar predictions."

DIANA-TarBase v7.0

TarBase houses a manually curated collection of experimentally tested miRNA targets in human, mouse, fruit fly, worm, and zebrafish, distinguishing between those that tested positive and those that tested negative [9]. TarBase version 7.0 contains more than half a million miRNA:gene interactions curated from published experiments on 356 different cell types from 24 species [10]. From University of Thessaly, Greece.

Arabidopsis small RNA data

Arabidopsis small RNA data includes information about Arabidopsis thaliana microRNAs, in addition to other small RNA molecules [11]. The most recent version was released on June 13, 2013.

InsecTar: Database for MicroRNA Targets in Insect

InsecTar (insectar.sanbi.ac.za/index.html) maintains a database of microRNAs in three disease-causing mosquito types: Anopheles gambiae (malaria, with 65 miRNAs), Aedes aegypti (dengue fever, yellow fever and other diseases, with more than 100 miRNA genes), Culex quinquefasciatus (many human and wild animal diseases, including West Nile, Rift Valley fever and St. Louis encephalitis, with more than 90 miRNA genes). Also included are the predicted targets of these miRNAs. By South African National Bioinformatics Institute.

miRGen

miRGen (diana.cslab.ece.ntua.gr/mirgen/index.php?r=mirgen/downloads) miRGen is an integrated database of: (i) positional relationships between animal miRNAs and genomic annotation sets, (ii) animal miRNA targets according to combinations of widely used target prediction programs [12]. The same group of researchers also provide TarBase and microT. The most recent bulk download is from 2009.

STarMirDB

STarMirDB from Wadsworth in the New York state, includes a collection of microRNA binding sites, predicted with STarMir algorithm (see below) [13]. In addition, some of the predictions supported with actual CLIP data are indicated.

Vir-Mir:

Vir-Mir (alk.ibms.sinica.edu.tw/cgi-bin/miRNA/miRNA.cgi) a database containing predicted viral miRNA candidate hairpins [14]. From Institute of BioMedical Science, Academia Sinica, Taipei, Taiwan. The site appears to be last updated in 2007.

Vita

ViTa (vita.mbc.nctu.edu.tw) is a collection of viral data from miRBase and ICTV, VirGne, VBRC.., etc, including known miRNAs on virus and supporting predicted host miRNA targets by miRanda and TargetScan [15]. ViTa also provide effective annotations, including human miRNA expression, virus infected tissues, etc. From Institute of Bioinformatics, National Chiao Tung University, Hsinchu, Taiwan. The site appears to be last updated in 2007.

miRGator 3.0

miRGator (http://mirgator.kobic.re.kr/) The miRGator database is a navigator tool for functional interpretation of miRNAs [16, 17]. Functional analyses and expression profiling are integrated with target gene prediction to infer biological function of miRNAs. Version 3.0 contains 73 deep sequencing datasets on human samples from GEO, SRA, and TCGA archives with 4.1 billion short reads and 2.5 billion aligned reads. From Ewha Womans University, Seoul, KOREA.

PolymiRTA 3.0: Polymorphism in microRNA Target Sites

PolymiRTS from University of Tennessee Health Science Center, United States is a database of naturally occurring DNA variations in both predicted and validated miRNA target sites [18]. The data can be searched or downloaded.

TransmiR

TransmiR (cmbi.bjmu.edu.cn/transmir) is a database for transcriptional regulation of microRNA by transcription factors [19]. From Beijing University, China. The most recent version 1.2, updated on 2013-1-30, contains 735 entries, which include ~201 transcriptional factors (TFs), ~209 miRNAs, and 16 organisms from 268 publications.

miR2Disease

miR2Disease (www.mir2disease.org) catalogs microRNA-disease relationship [20]. It is a manually curated database about microRNA information related to human diseases. From Harbin Institue of Technology, China. The database was last updated on March 14, 2011, and contains 349 miRNAs, 163 diseases, and a total of 3273 entries.

CoGeMiR: Comparative Genomics Analysis of MicroRNA

CoGeMiR (cogemir.tigem.it/) CoGeMiR offers an overview of the conservation of microRNAs during evolution in different animal species [21]. This database collects information on genomic location, conservation and expression data of both known and predicted microRNAs. From The Telethon Institute of Genetics and Medicine, Italy. The latest release was in June 2008. On the date of evaluation, the site is not operational.

S-MED: Sarcoma - microRNA Expression Database

S-MED (www.oncomir.umn.edu/SMED/index.php) is a repository of expression data for microRNAs in different types of human sarcoma tumor and select normal tissues. From University of Minnesota, United States.

others
  • ChIPBase: a database for decoding the transcriptional regulation of long non-coding RNA and microRNA genes from ChIP-Seq data [22].
  • miRCancer: a microRNA–cancer association database constructed by text mining on literature [23].
  • YM500: a small RNA sequencing (smRNA-seq) database for microRNA research [24].
  • HMDD v2.0: a database for experimentally supported human microRNA and disease associations [25].
  • starBase v2.0: decoding miRNA-ceRNA, miRNA-ncRNA and protein–RNA interaction networks from large-scale CLIP-Seq data [26].
  • PMTED: a plant microRNA target expression database [27].
  • PASmiR: a literature-curated database for miRNA molecular regulation in plant response to abiotic stress [28]
  • OncomiRDB: a database for the experimentally verified oncogenic and tumor-suppressive microRNAs [29]
microRNA target prediction software
miRSystem

miRSystem integrates the other target predication softwares: DIANA, miRanda, miRBridge, PicTar, PITA, rna22, and TargetScan., and contains validated data from TarBase and miRecords [30]. The database only supports human and mouse. The most recent version was release in May 2014.

STarMir

STarMir from Wadsworth is a software program [31], based on the sequence, thermodynamic and target structure features derived from CLIP data [13].

miRDB

miRDB (mirdb.org/miRDB/) is an online microRNA target prediction database. All targets are predicted by MirTarget, which employs SVM learning machine to analyze thousands of miRNA and target interactions [32]. Current version 5.0, released in August 2014, is based on miRBase version 21 with MirTarget V3, involves 6709 microRNAs from human, mouse, rat, dog, and chicken, with the total number of predicted targets of 2,105,008. The whole data set can be downloaded.

TargetScan

TargetScan (www.targetscan.org/) predicts biological targets of miRNAs by searching for the presence of conserved 8mer and 7mer sites that match the seed region of each miRNA [33]. It is from the Informatics and Research Computing, Whitehead Institute for Biomedical Research, United States. Most recent release is version 6.2 in June 2012. The main home page is for mammalian target prediction. Mouse, worm, fly, and fish have separate search page links on the home page.

PICTAR

PicTar (www.pictar.org/) PicTar is an algorithm for the identification of microRNA targets [34]. This searchable website provides details regarding: microRNA target predictions in vertebrates, seven Drosophila species,three nematode species, and human microRNA targets that are not conserved but co-expressed (i.e. the microRNA and mRNA are expressed in the same tissue). From Rajewsky lab at NYU's Center for Comparative Functional Genomics and the Max Delbruck Centrum, Berlin, Germany.

Diana-microT

Diana-microT (diana.cslab.ece.ntua.gr/microT/) currently is in its 5th version [35]. The webpage indicates that it has the "highest sensitivity at any level of specificity, when compared against other state of the art implementations". "It also provides hyperlinks to on-line servers such as iHOP and expression data for the selected microRNAs in tissues and cell lines" and also link to KEGG pathways. The full dataset of predicted human and mouse target sites can be downloaded. The most recent version was built in July 2012.

RNA22

RNA22 [36, 37] is available from Computational Medicine Center, Thomas Jefferson University.

RNA22 (cbcsrv.watson.ibm.com/rna22.html) initially ran from the IBM Watson Computational Biology Center. As of October 20, 2012, the website does not appear to be funtional.

TripletSVM

TripletSVM (bioinfo.au.tsinghua.edu.cn/mirnasvm/) predicts a query sequence with hairpin structure as a real miRNA precursor or not [38]. The program is trained with the triplet element features of a set of real miRNA precursors and a set of pseudo-miRNA hairpins. From Tsinghua University, Beijing, China. The software is free for download.

miRanda - microRNA.org

The software miRanda is a part of microRNA.org (www.microrna.org/), which is a resource for predicted microRNA targets for human, mouse, rat, drosophila and Caenorhabditis elegans genomes, and also provides the expression profile of miRNA in various tissues [39]. It is from Computational Biology Center at Memorial Sloan-Kettering Cancer Center (MSKCC) in the United States. The site was last update in August 2010.

RNAhybrid

RNAhybrid (bibiserv.techfak.uni-bielefeld.de/rnahybrid/) is a tool for finding the minimum free energy hybridisation of a long and a short RNA [40]. The hybridisation is performed in a kind of domain mode, ie. the short sequence is hybridized to the best fitting part of the long one. The tool serves as microRNA target prediction. From Universität Bielefeld, Germany.

PITA

PITA (genie.weizmann.ac.il/pubs/mir07/mir07_prediction.html) is a target prediction platform [41]. The last released catalog of predicted microRNA targets was on August 31, 2008, based on miRBase release 11.

Users can input UTR sequences into the web form to search for the predicted target sites, or download the executable to use locally.

other microRNA-related software
DIANA-mirExTra

DIANA-mirExTra From DIANA lab at the B.S.R.C. “Alexander Fleming”. The algorithm compares two lists of mRNA genes, one changed, and one unchanged, and seek to identify any hexamers in the 3' untranslated regions whose presence in the list of changed genes is statistically significant [42]. The involvement of miRNAs can be loosely identified through those hexamers. An alternative approach based on miRNA target prediction scores instead of hexamer frequencies can also be used.

WMD3: Web MicroRNA Designer

WMD3 (wmd3.weigelworld.org) designs artificial microRNAs (amiRNAs) [43, 44]. The 21mer amiRNA21mers can specifically silences single or multiple genes of interest in more than 90 plants. From Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany. It appears to be last updated in 2009.

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ISSN : 2329-5139