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A comparative account of microRNA resources, feature-validations and application-based categorizations : SPECIES: rat
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
miRWalk
http://mirwalk.uni-hd.de/
Database of predicted and validated microRNAs.
Dweep H, Sticht C, Pandey P, Gretz N. miRWalk - Database: Prediction of possible miRNA binding sites by "walking" the genes of three genomes. J Biomed Inform. 2011 May 14. [Epub ahead of print] PubMed PMID: 21605702.
2011
94
The ARGONAUTE database was incorporated in miRWalk.
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
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.
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
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
Tool by Vinod Chandra et al.,(2009)
URL not found
In silico tool for pre-microRNA classification by using structural and thermodynamic motifs.
Vinod Chandra, S.S., Reshmi, G.; A pre-microRNA classifier by structural and thermodynamic motifs, Nature & Biologically Inspired Computing, 2009. NaBIC 2009.
2009
100
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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