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A comparative account of microRNA resources, feature-validations and application-based categorizations : SPECIES: mouse
Resources Important features / utilities*CitationsYear of publicationRank by usage frequency Click to Edit / Add comments
vHoT
http://dna.korea.ac.kr/vhot.
vHoT database predicts interspecies interactions between viral microRNA and host genomes.
Kim H, Park S, Min H, Yoon S.vHoT: a database for predicting interspecies interactions between viral microRNA and host genomes.Arch Virol. 2012 Mar;157(3):497-501. doi: 10.1007/s00705-011-1181-y.PMID: 22160653
2012
50
miRBase
http://www.mirbase.org/
A major microRNA repository comprising of microRNA sequences and annotation obtained from published literature wherein both precursor and mature sequences can be retrieved from the database.
Kozomara A, Griffiths-Jones S. miRBase: integrating microRNA annotation and deep-sequencing data. Nucleic Acids Res. 2011 Jan;39(Database issue):D152-7. Epub 2010 Oct 30. PubMed PMID: 21037258 Griffiths-Jones S, Saini HK, van Dongen S, Enright AJ. miRBase: tools for microRNA genomics. Nucleic Acids Res. 2008 Jan;36(Database issue):D154-8. Epub 2007 Nov 8. PubMed PMID: 17991681
2011
66
miRNA_Targets
http://mamsap.it.deakin.edu.au/mirna_targets/.
miRNA_Targets database provide researchers a query platform to investigate miRNA interactions in non-coding and coding regions of RNA and promote research activity on neglected 5? and coding regions of mRNA.
Kumar A, Wong AK, Tizard ML, Moore RJ, Lefèvre C.miRNA Targets:A database for miRNA target predictions in coding and non-coding regions of mRNAs.Genomics. 2012 Dec;100(6):352-6. doi: 10.1016/j.ygeno.2012.08.006. PMID: 22940442.
2012
76
Argonaute
http://www.ma.uniheidelberg.de/apps/zmf/argonaute/interface
Argonaute hosts additional information on the origin of an miRNA, i.e. in which host gene it is encoded, its expression in different tissues and its known or proposed function, its potential target genes including Gene Ontology annotation, as well as miRNA families and proteins known to be involved in miRNA processing.
Shahi P, Loukianiouk S, Bohne-Lang A, Kenzelmann M, Küffer S, Maertens S, Eils R, Gröne HJ, Gretz N, Brors B.Argonaute--a database for gene regulation by mammalian microRNAs.Nucleic Acids Res. 2006 Jan 1;34(Database issue):D115-8PMID: 16381827
2006
85
Genecopoeia
http://www.genecopoeia.com/product/mirna/
Provides tools and resources for EXPERIMENTAL data analysis of microRNAs such as detection, expression, validation or knockout studies.
Not available
Not available
97
miRDB
http://mirdb.org
Database on predicted microRNA targets and functional annotations of especially mature microRNA in animals.
Wang X. miRDB: a microRNA target prediction and functional annotation database with a wiki interface. RNA. 2008 Jun;14(6):1012-7. Epub 2008 Apr 21. PubMed PMID: 18426918
2008
97
Dataset downloadable
APADB
http://tools.genxpro.net/apadb/.
Müller S, Rycak L, Afonso-Grunz F, Winter P, Zawada AM, Damrath E,Scheider J, Schmäh J, Koch I, Kahl G, Rotter B.APADB: A database for alternative polyadenylation and microRNA regulation events. Database (Oxford). 2014 Jul 22;2014. pii: bau076. doi: 10.1093/database/bau076. PMID: 25052703.
2014
100
Argonaute database
1. http://www.umm.uni-heidelberg.de/apps/zmf/mirwalk/ 2. http://www.ma.uni-heidelberg.de/apps/zmf/argonaute/interface
Provides information on mammalian microRNAs, their coding regions and regulatory aspects of their targeted genes.
Shahi P, Loukianiouk S, Bohne-Lang A, Kenzelmann M, Küffer S, Maertens S, Eils R, Gröne HJ, Gretz N, Brors B. Argonaute--a database for gene regulation by mammalian microRNAs. Nucleic Acids Res. 2006 Jan 1;34(Database issue):D115-8. PubMed PMID: 16381827; PubMed Central PMCID: PMC1347455.
2006
100
The ARGONAUTE database has been incorporated in a new internet-based resource called miRWalk.
Diana micro T
1. http://www.microrna.gr/microT 2. http:www.microrna.gr/microT-v4
Computational analysis of microRNA targets by using conserved and non-conserved microRNA recognition elements to derive the prediction score.
1. Maragkakis M, Vergoulis T, Alexiou P, Reczko M, Plomaritou Maragkakis M, Reczko M, Simossis VA, Alexiou P, Papadopoulos GL, Dalamagas T, Giannopoulos G, Goumas G, Koukis E, Kourtis K, Vergoulis T, Koziris N, Sellis T, Tsanakas P, Hatzigeorgiou AG. DIANA-microT web server: elucidating microRNA functions through target prediction. Nucleic Acids Res. 2009 Jul;37(Web Server issue):W273-6. Epub 2009 Apr 30. PubMed PMID: 19406924K,
2009
100
DIANA-LncBase
www.microrna.gr/LncBase
DIANA-LncBase hosts transcriptome-wide experimentally verified and computationally predicted miRNA recognition elements (MREs) on human and mouse lncRNAs.
Paraskevopoulou MD, Georgakilas G, Kostoulas N, Reczko M, Maragkakis M, Dalamagas TM,Hatzigeorgiou AG.Nucleic Acids Res. 2013 Jan;41(Database issue):D239-45. doi: 10.1093/nar/gks1246.PMID: 23193281
2013
100
EpimiR
http://bioinfo.hrbmu.edu.cn/EpimiR/. Go to: Introduction
EpimiR provides a fairly comprehensive repository about the mutual regulation between epigenetic modifications and miRNAs, which will promote the research on the regulatory mechanism of epigenetics and miRNA
Dai E, Yu X, Zhang Y, Meng F, Wang S, Liu X, Liu D, Wang J, Li X, Jiang W.EpimiR: A database of curated mutual regulation between miRNAs and epigenetic modifications.Database (Oxford). 2014 Mar 28;2014:bau023. doi: 10.1093/database/bau023.PMID: 24682734
2014
100
EpimiRBase
http://www.epimirbase.eu
This database includes information on up- and down-regulated microRNAs in the brain and blood,as well as functional studies, and covers both rodent models and human epilepsy.
Mooney C, Becker BA, Raoof R, Henshall DC.EpimiRBase: A comprehensive database of EpimiRBase: A comprehensive database of microRNA-epilepsy associations.Bioinformatics. 2016 May 1;32(9):1436-8. doi: 10.1093/bioinformatics/btw008.PMID:26748106.
2016
100
GeneHub-GEPIS
1. http://research-public.gene.com/ 2.http://research-public.gene.com/Research/genentech/genehub-gepis/index.html 3. http://www.cgl.ucsf.edu/Research/genentech/genehub-gepis/
GeneHub-GEPIS is a bioinformatic tool for inferring gene expression patterns in a large panel of normal and cancer tissues based on human and mouse EST sequence abundance.
Zhang Y, Luoh SM, Hon LS, Baertsch R, Wood WI, Zhang Z. GeneHub-GEPIS: digital expression profiling for normal and cancer tissues based on an integrated gene database. Nucleic Acids Res. 2007 Jul;35(Web Server issue):W152-8. Epub 2007 Jun 1. PubMed PMID: 17545196
2007
100
Datasets downloadable
IntmiR
http://210.212.237.35/intmir/
Database of published intronic microRNAs in human and mouse providing details on their targets, pathways, altered functioning in disease states or affected tissues.
Girijadevi R, Sreedevi VC, Sreedharan JV, Pillai MR. IntmiR: a complete catalogue of intronic miRNAs of human and mouse. Bioinformation. 2011 Feb 15;5(10):458-9. PubMed PMID: 21423893; PubMed Central PMCID: PMC3055153.
2011
100
mESAdb
http://konulab.fen.bilkent.edu.tr/mirna/
The database primarily comprises mature microRNA sequences and their target data along with selected human, mouse and zebrafish expression data sets. doi: 10.1093/nar/gkq1256. PMID: 21177657
Kaya KD, Karakülah G, Yakicier CM, Acar AC, Konu O.mESAdb: microRNA expression and sequence analysis database.Nucleic Acids Res. 2011 Jan;39(Database issue):D170-80.
2011
100
mESAdb- microRNA expression and sequence analysis database
http://konulab.fen.bilkent.edu.tr/mirna/
microRNA expression and sequence analysis database essentially provides information of mature microRNA sequences and their targets.
Kaya KD, Karakülah G, Yakicier CM, Acar AC, Konu O. mESAdb: microRNA expression and sequence analysis database. Nucleic Acids Res. 2011 Jan;39(Database issue):D170-80. PubMed PMID: 21177657
2011
100
Access to complete set of tools requires login and registration
microPIR2
http://www4a.biotec.or.th/micropir2
Piriyapongsa J, Bootchai C, Ngamphiw C, Tongsima S.microPIR2: A comprehensive database for human mouse comparative study of microRNA promoter interactions.Database (Oxford). 2014 Nov 25;2014:bau115. doi: 10.1093/database/bau115.PMID: 25425035
2014
100
microTranspoGene
http://transpogene.tau.ac.il/microTranspoGene.html
Database of microRNAs that are derived from transposable elements.
Levy A, Sela N, Ast G. TranspoGene and microTranspoGene: transposed elements influence on the transcriptome of seven vertebrates and invertebrates. Nucleic Acids Res. 2008 Jan;36(Database issue):D47-52. Epub 2007 Nov 5. PubMed PMID: 17986453; PubMed Central PMCID: PMC2238949.
2008
100
Dataset downloadable
miRex
http://miracle.igib.res.in/mirex/
Web based resource which assists users to evaluate and study gene expression and also serves as an online repository for microRNA gene expression data.
Bargaje R, Hariharan M, Scaria V, Pillai B. Consensus miRNA expression profiles derived from interplatform normalization of microarray data. RNA. 2010 Jan;16(1):16-25. Epub 2009 Nov 30. PubMed PMID: 19948767; PubMed Central PMCID: PMC2802026.
2010
100
miRGator, miRGator v2.0
1. http://genome.ewha.ac.kr/miRGator/ 2. http://miRGator.kobic.re.kr 3. http://mirgator.kobic.re.kr:8080/MEXWebApp/
An integrated database for functional annotation of microRNA that includes expression, regulation, function, pathway,pathological or disease terms as well as microRNA targeting (miRanda, picTar and TargetScan).
Nam S, Kim B, Shin S, Lee S. miRGator: an integrated system for functional annotation of microRNAs. Nucleic Acids Res. 2008 Jan;36(Database issue):D159-64. Epub 2007 Oct 16. PubMed PMID: 17942429
2008
100
miRHrt
http://sysbio.suda.edu.cn/mirhrt/
Database of microRNA regulating heart development.
Liu G, Ding M, Chen J, Huang J, Wang H, Jing Q, Shen B. Computational analysis of microRNA function in heart development. Acta Biochim Biophys Sin (Shanghai). 2010 Sep;42(9):662-70. Epub 2010 Aug 17. PubMed PMID: 20716610.
2010
100
Dataset downloadable. On querying each section, no results were obtained and the following message was displayed:"Can't connect to MySQL server "(30-3-12, 7-4-12, 22-4-12, 24-4-12,29-6-12 , 18-7-12 ).
mirKO
http://www.knockoutmouse.org/martsearch
Mouse microRNA knockout resource is a collection of mutant embryonic stem cells harboring specific deletions for most of the microRNA genes reposited in miRBase.
Prosser HM, Koike-Yusa H, Cooper JD, Law FC, Bradley A. A resource of vectors and ES cells for targeted deletion of microRNAs in mice. Nat Biotechnol. 2011 Aug 7;29(9):840-5. doi: 10.1038/nbt.1929. PubMed PMID: 21822254; PubMed Central PMCID: PMC3242032.
2011
100
miRmap web
http://mirmap.ezlab.org.
Vejnar CE, Blum M, Zdobnov EM.Comprehensive microRNA target prediction online.Nucleic Acids Res. 2013 Jul;41(Web Server issue):W165-8. doi: 10.1093/nar/gkt430.PMID: 23716633
2013
100
miRNAMap, miRNAMap 2.0
1. http://mirnamap.mbc.nctu.edu.tw/
Genomic network of microRNAs in metazoan genomes that are beneficial in inferring microRNA regulatory functions. miRNAMap 2.0, was developed to retrieve and store details of experimentally verified microRNAs and experimentally verified microRNA target genes in human, mouse, rat, and other metazoan genomes.
Hsu PW, Huang HD, Hsu SD, Lin LZ, Tsou AP, Tseng CP, Stadler PF, Washietl S, Hofacker IL. miRNAMap: genomic maps of microRNA genes and their target genes in mammalian genomes. Nucleic Acids Res. 2006 Jan 1;34(Database issue):D135-9. PubMed PMID: 16381831
2006
100
miRNApath
http://lgmb.fmrp.usp.br/mirnapath
Web based resource to study the role of microRNAs and the genes regulated by them, especially in metabolic pathways .
A.O. Chiromatzo1, T.Y.K. Oliveira1, G. Pereira1, A.Y. Costa2, C.A.E. Montesco3, D.E. Gras1, F. Yosetake4, J.B. Vilar5, M. Cervato4, P.R.R. Prado1, R.G.C.C.L. Cardenas4, R. Cerri6, R.L. Borges4, R.N. Lemos4, S.M. Alvarenga7, V.R.C. Perallis6, D.G. Pinheiro1, I.T. Silva1, R.M. Brandão1, M.A.V. Cunha1, S. Giuliatti1 and W.A. Silva Jr1 miRNApath: a database of miRNAs, target genes and metabolic pathways, Genet. Mol. Res. 6 (4): 859-865 (2007) October 05, 2007
2007
100
miRNEST
http://mirnest.amu.edu.pl
Comprehensive database on animal, plant and virus microRNA including details on species that are of importance in medical and agricultural research.
Szczesniak MW, Deorowicz S, Gapski J, Kaczynski L, Makalowska I. miRNEST database: an integrative approach in microRNA search and annotation. Nucleic Acids Res. 2012 Jan;40(Database issue):D198-204. Epub 2011 Dec 1. PubMed PMID: 22135287; PubMed Central PMCID: PMC3245016.
2012
100
miRNeye
http://mirneye.tigem.it/
Mouse eye atlas depicting the expression pattern and location of 221 microRNAs in developing and adult mouse
Karali M, Peluso I, Gennarino VA, Bilio M, Verde R, Lago G, Dollé P, Banfi S. miRNeye: a microRNA expression atlas of the mouse eye. BMC Genomics. 2010 Dec 20;11:715. PubMed PMID: 21171988; PubMed Central PMCID: PMC3018480.
2010
100
miRSel
http://services.bio.ifi.lmu.de/mirsel
Database of microRNA-gene associations derived from mining of data from biomedical literature.
Naeem H, Küffner R, Csaba G, Zimmer R. miRSel: automated extraction of associations between microRNAs and genes from the biomedical literature. BMC Bioinformatics. 2010 Mar 16;11:135. PubMed PMID: 20233441; PubMed Central PMCID: PMC2845581.
2010
100
miRSponge
http://www.bio-bigdata.net/miRSponge
miRSponge, a manually curated database, which aims at providing an experimentally supported resource for microRNA (miRNA) sponges.
Wang P, Zhi H, Zhang Y, Liu Y, Zhang J, Gao Y, Guo M, Ning S, Li X.miRSponge: a manually curated database for experimentally supported miRNA sponges and ceRNAs.Sci Rep. 2016 Mar 24;6:23700. doi: 10.1038/srep23700.PMID: 26424084.
2016
100
miTALos
1. http://mips.helmholtz-muenchen.de/mitalos/index.jsp 2. http://hmgu.de/cmb/mitalos
Web based resource on microRNA-directed regulation of signaling pathways in human and mouse developed by the integration of five different microRNA target prediction tools:TargetScan, RNA22, TargetSpy, PITA and PicTar and two different signaling pathway resources (KEGG and NCI: National Cancer Institute Pathway Interaction Database).
Kowarsch A, Preusse M, Marr C, Theis FJ. miTALOS: analyzing the tissue-specific regulation of signaling pathways by human and mouse microRNAs. RNA. 2011 May;17(5):809-19. Epub 2011 Mar 25. PubMed PMID: 21441347; PubMed Central PMCID: PMC3078731.
2011
100
Downloadable on request
Musmirus
http://www.kimmelcancercenter.org/siracusa/musmirsus.htm
Musmirus database was developed to compare the location of microRNA genes with the location of solid tumor susceptibility and modifier loci in the mouse.
Not available
Not available
100
The MUSMIRSUS database is maintained by Dr. Linda D. Siracusa, Dr. Cinzia Sevignani, and Stephanie Nnadi at Thomas Jefferson University, 233 South 10th Street, Philadelphia, PA 19107.
omiRas
http://tools.genxpro.net/omiras/.
It gives static annotation results including length distribution, mapping,statistics, alignments and quantification tables for each library as well as lists of differentially expressed ncRNAs.
Müller S, Rycak L, Winter P, Kahl G, Koch I, Rotter B.omiRas: a Web server for differential expression analysis of miRNAs derived from small RNA-Seq data.Bioinformatics. 2013 Oct 15; 29(20):2651-2. doi: 10.1093/bioinformatics/btt457.PMID: 23946503
2013
100
RBPmap
http://rbpmap.technion.ac.il/
RBPmap enables the users to select motifs from a large database of experimentally defined motifs. RBPmap incorporates a position-specific background model, designed uniquely for different genomic regions, such as splice sites, 5’ and 3’ UTRs, non-coding RNA and intergenic regions.
Inbal Paz, 1 Idit Kosti, 1 Manuel Ares, Jr, 2 Melissa Cline, 3 and Yael Mandel-Gutfreund.RBPmap: A web server for mapping binding sites of RNA-binding proteins. Nucleic Acids Res. 2014 Jul 1; 42(Web Server issue): W361–W367. PMCID: PMC4086114
2014
100
RepTar
http://reptar.ekmd.huji.ac.il
Database on genome-wide computed details of human and mouse microRNAs as well as of cellular targets of human and mouse viral microRNAs.
Elefant N, Berger A, Shein H, Hofree M, Margalit H, Altuvia Y. RepTar: a database of predicted cellular targets of host and viral miRNAs. Nucleic Acids Res. 2011 Jan;39(Database issue):D188-94. Epub 2010 Dec 10. PubMed PMID: 21149264
2010
100
Dataset downloadable
RepTar
http://reptar.ekmd.huji.ac.il.
It is based on the RepTar algorithm that is independent of evolutionary conservation considerations and is not limited to seed pairing sites.
Elefant N, Berger A, Shein H, Hofree M, Margalit H, Altuvia Y.RepTar: A database of predicted cellular targets of host and viral miRNAs.Nucleic Acids Res.2011 Jan;39(Database issue):D188-94. doi: 10.1093/nar/gkq1233.PMID: 21149264
2011
100
SM2miR
http://bioinfo.hrbmu.edu.cn/SM2miR/.
It collects and incorporates the experimentally validated small molecules' effects on miRNA expression in 20 species from the published papers. experimentally validated small molecules' effects on microRNA expression. Bioinformatics. 2013 Feb 1;29(3):409-11. doi: 10.1093/bioinformatics/bts698. PMID: 23220571
Liu X, Wang S, Meng F, Wang J, Zhang Y, Dai E, Yu X, Li X, Jiang W.SM2miR-a database of the
2013
100
smiRNAdb
http://www.mirz.unibas.ch/cloningprofiles/
Online resource for expression information on small RNAs (mostly miRNAs) for human, mouse, rat, zebrafish, worm and fruitfly.
Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S, Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V, Chiaretti S, Foà R, Schliwka J, Fuchs U, Novosel A, Müller RU, Schermer B, Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G, Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN, Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo JJ, Sander C, Zavolan M, Tuschl T. A mammalian microRNA expression atlas based on small RNA library sequencing. Cell. 2007 Jun 29;129(7):1401-14. PubMed PMID: 17604727; PubMed Central PMCID: PMC2681231.
2007
100
Datasets downloadable
SomamiR
http://compbio.uthsc.edu/SomamiR/
The database contains a collection of germline and somatic mutations in miRNAs and their targets that have been experimentally shown to impact miRNA function and have been associated with cancer.
Bhattacharya A, Ziebarth JD, Cui Y.SomamiR-a database for somatic mutations impacting microRNA function in cancer. Nucleic Acids Res. 2013 Jan;41(Database issue):D977-82. doi: 10.1093/nar/gks1138. PMID:23180788
2013
100
TargetRank
http://genes.mit.edu/targetrank/
Computational tool to identify microRNA target sites based on several parameters such as seed match (many types), AU content, presence of A or U at position t9 etc.
Nielsen CB, Shomron N, Sandberg R, Hornstein E, Kitzman J, Burge CB. Determinants of targeting by endogenous and exogenous microRNAs and siRNAs. RNA. 2007 Nov;13(11):1894-910. Epub 2007 Sep 13. PubMed PMID: 17872505; PubMed Central PMCID: PMC2040081.
2007
100
Dataset downloadable
 
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