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A comparative account of microRNA resources, feature-validations and application-based categorizations : SPECIES: worm
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
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
EIMMO
1.http://piech.kaist.ac.kr/dynamod 2. http://biocondor6.kaist.ac.kr/dynamod/
Tool for microRNA target prediction and enrichment and depletion analysis in Gene Ontology terms.
Gaidatzis D, van Nimwegen E, Gaidatzis D, van Nimwegen E, Hausser J, Zavolan M. Inference of miRNA targets using evolutionary conservation and pathway analysis. BMC Bioinformatics. 2007 Mar 1;8:69. Erratum in: BMC Bioinformatics. 2007 Jul 12;8(1):248. PubMed PMID: 17331257
2007
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
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
UTRome.org
http://www.UTRome.org
Web based resource on 3'UTR biology in C. elegans
Mangone M, Macmenamin P, Zegar C, Piano F, Gunsalus KC. UTRome.org: a platform For 3' UTR biology in C. elegans. Nucleic Acids Res. 2008 Jan;36(Database issue):D57-62. Epub 2007 Nov 5. PubMed PMID: 17986455; PubMed Central PMCID: PMC2238901.
2008
100
Dataset downloadable
 
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