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A comparative account of microRNA resources, feature-validations and application-based categorizations : SPECIES: zebrafish
Resources Important features / utilities*CitationsYear of publicationRank by usage frequency Click to Edit / Add comments
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
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
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
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 ).
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
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
Vir-Mir-db
http://alk.ibms.sinica.edu.tw
Web based resource that allows a user to explore predicted viral microRNA hairpins and their corresponding host target gene.
Li SC, Shiau CK, Lin WC. Vir-Mir db: prediction of viral microRNA candidate hairpins. Nucleic Acids Res. 2008 Jan;36(Database issue):D184-9. Epub 2007 Aug 15. PubMed PMID: 17702763
2008
100
 
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