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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
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
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.

The ARGONAUTE database was incorporated in miRWalk.
Provides tools and resources for EXPERIMENTAL data analysis of microRNAs such as detection, expression, validation or knockout studies.
Not available
Not available
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

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.

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
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
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.
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.

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.
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
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