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A comparative account of microRNA resources, feature-validations and application-based categorizations : SPECIES: human
Resources Important features / utilities*CitationsYear of publicationRank by usage frequency Click to Edit / Add comments
MicroPred
1. http://www.cs.ox.ac.uk/people/manohara.rukshan.batuwita/microPred.htm 2. http://web.comlab.ox.ac.uk/people/ManoharaRukshan.Batuwita/microPred.htm.
Computational tool which can be utilized for determining pseudo and real human precursor microRNAs
Batuwita R, Palade V. microPred: effective classification of pre-miRNAs for human miRNA gene prediction. Bioinformatics. 2009 Apr 15;25(8):989-95. Epub 2009 Feb 20. PubMed PMID: 19233894.
2009
50
To be validated.
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
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
miR2Disease
http://www.miR2Disease.org
A web-based resource on human microRNAs and their role in disease states obtained from manually curated data.
Jiang Q, Wang Y, Hao Y, Juan L, Teng M, Zhang X, Li M, Wang G, Liu Y. miR2Disease: a manually curated database for microRNA deregulation in human disease. Nucleic Acids Res. 2009 Jan;37(Database issue):D98-104. Epub 2008 Oct 15. PubMed PMID: 18927107
2008
99
Dataset downloadable
Antagomirbase
http://bioinfopresidencycollegekolkata.edu.in/antagomirs.html
Web-based resource of predicted putative antagomirs that are directed against human microRNA.
Ganguli S, Mitra S, Datta A. Antagomirbase- a putative antagomir database. Bioinformation. 2011;7(1):41-3. Epub 2011 Aug 20. PubMed PMID: 21904438; PubMed Central PMCID: PMC3163932.
2011
100
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
CePred
http://cmbi.bjmu.edu.cn/cepred/
Tool for determining the likelihood of expression of intronic microRNAs along with their host gene.
Wang D, Lu M, Miao J, Li T, Wang E, Cui Q. Cepred: predicting the co-expression patterns of the human intronic microRNAs with their host genes. PLoS One. 2009;4(2):e4421. Epub 2009 Feb 10. PubMed PMID: 19204784
2009
100
CID-miRNA
http://mirna.jnu.ac.in/cidmirna/.
CID-miRNA, identifies miRNA precursors in a given DNA sequence, utilising secondary structure-based filtering systems.
Tyagi S, Vaz C, Gupta V, Bhatia R, Maheshwari S, Srinivasan A, Bhattacharya A. CID-miRNA: A web server for prediction of novel miRNA precursors in human genome.Biochem Biophys Res Commun. 2008 Aug 8;372(4):831-4. doi: 10.1016/j.bbrc.2008.05.134.PMID: 18522801.
2008
100
CircInteractome
http://circinteractome.nia.nih.gov
Not available
2016
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
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
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
ExprTarget
http://www.scandb.org/apps/microrna/
Computational tool for predicting human microRNA targets by integrating methods such as miRanda, PicTar, TargetScan as well as the genome-wide HapMap miRNA and mRNA expression data sets which were generated in the authors laboratory.
Gamazon ER, Im HK, Duan S, Lussier YA, Cox NJ, Dolan ME, Zhang W. Exprtarget: an integrative approach to predicting human microRNA targets. PLoS One. 2010 Oct 21;5(10):e13534. PubMed PMID: 20975837; PubMed Central PMCID: PMC2958831.
2010
100
F-SNP
http://compbio.cs.queensu.ca/F-SNP
A collection of functional SNPs that are exclusively segregated for analytical studies in disease conditions.
Lee PH, Shatkay H. An integrative scoring system for ranking SNPs by their potential deleterious effects. Bioinformatics. 2009 Apr 15;25(8):1048-55. Epub 2009 Feb 19. PubMed PMID: 19228803.
2009
100
G-DOC
https://gdoc.georgetown.edu.
Web based resource for cancer related studies that incorporates and integrates data on clinical findings of patients, their results and data from large scale studies.
Madhavan S, Gusev Y, Harris M, Tanenbaum DM, Gauba R, Bhuvaneshwar K, Shinohara A, Rosso K, Carabet LA, Song L, Riggins RB, Dakshanamurthy S, Wang Y, Byers SW, Clarke R, Weiner LM. G-DOC: a systems medicine platform for personalized oncology. Neoplasia. 2011 Sep;13(9):771-83. PubMed PMID: 21969811; PubMed Central PMCID: PMC3182270.
2011
100
Requires registration which is free of cost.
GIFts- GeneCards Inferred Functionality Scores
http://www.genecards.org/GIFtS.shtml
Computational tool designed to perform functional analysis of a wide set of genes derived from experimental data or in silico analysis.
Harel A, Inger A, Stelzer G, Strichman-Almashanu L, Dalah I, Safran M, Lancet D. GIFtS: annotation landscape analysis with GeneCards. BMC Bioinformatics. 2009 Oct 23;10:348. PubMed PMID: 19852797; PubMed Central PMCID: PMC2774327.
2009
100
Open access for academic and non commercial users
HMDD - Human microRNA disease database
1. http://202.38.126.151/hmdd/mirna/md/ 2. http://cmbi.bjmu.edu.cn/hmdd
Database of experimentally verified microRNA and their relationship to disease states
Lu M, Zhang Q, Deng M, Miao J, Guo Y, Gao W, Cui Q. An analysis of human microRNA and disease associations. PLoS One. 2008;3(10):e3420. Epub 2008 Oct 15. PubMed PMID: 18923704
2008
100
Downloadable on request.
HNOCDB
http://gyanxet.com/hno.html.
Mitra S, Das S, Das S, Ghosal S, Chakrabarti J.HNOCDB: a comprehensive database of genes and miRNAs relevant to head and neck and oral cancer. Oral Oncol. 2012 Feb;48(2):117-9. doi: 10.1016/j.oraloncology.2011.09.014.PMID: 22024348
2012
100
HOCTAR- Host gene oppositely correlated targets
http://hoctar.tigem.it
Host gene oppositely correlated targets is used for prediction of microRNA targets and functional relationship between microRNAs and their target genes, based on a scoring system developed by comparison with transcriptomic data.
Gennarino VA, Sardiello M, Mutarelli M, Dharmalingam G, Maselli V, Lago G, Banfi S. HOCTAR database: a unique resource for microRNA target prediction. Gene. 2011 Jul 1;480(1-2):51-8. Epub 2011 Mar 22. PubMed PMID: 21435384; PubMed Central PMCID: PMC3113163.
2011
100
HuMiTar
URL not found
Software application that enables identification of potential human microRNA targets.
Ruan J, Chen H, Kurgan L, Chen K, Kang C, Pu P. HuMiTar: a sequence-based method for prediction of human microRNA targets. Algorithms Mol Biol. 2008 Dec 22;3:16. PubMed PMID: 19102780; PubMed Central PMCID: PMC2631598.
2008
100
ImmunemiR
not found
The database provide a comprehensive repository of human immune disease associated miRNAs with network visualization options of its target genes, protein-protein interactions (PPI).
Prabahar A, Natarajan J.ImmunemiR- a database of prioritized immune miRNA disease associations and its reactome.microrna.PMID: 28124611
2017
100
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
Magia
http://gencomp.bio.unipd.it/magia/start/
Bioinformatic resource for comparative analysis of microRNA and target genes and study of gene expression profile.
Sales G, Coppe A, Bisognin A, Biasiolo M, Bortoluzzi S, Romualdi C. MAGIA, a web-based tool for miRNA and Genes Integrated Analysis. Nucleic Acids Res. 2010 Jul;38(Web Server issue):W352-9. Epub 2010 May 19. PubMed PMID: 20484379; PubMed Central PMCID: PMC2896126.
2010
100
MAGIA is freely available for academic users.
MAGIA
http://gencomp.bio.unipd.it/magia.
MAGIA is a novel web-based tool that allows to retrieve and browse updated miRNA target predictions for human miRNAs, based on a number of different algorithms (PITA, miRanda and TargetScan), with the possibility of combining them with Boolean operators.
Sales G, Coppe A, Bisognin A, Biasiolo M, Bortoluzzi S, Romualdi C.MAGIA: A web-based tool for miRNA and Genes Integrated Analysis.Nucleic Acids Res. 2010 Jul ;38(Web Server issue):W352-9. doi: 10.1093/nar/gkq423.PMID: 20484379
2010
100
MAMI- Meta Mir-target Inference
http://mami.med.harvard.edu/
Tool for determining potential targets of human microRNA and the association of expression and genome- wide microRNA profile.
Not available
Not available
100
After submitting the data for analysis, the results could not be accessed.(7-4-12, 22-4-12, 24-4-12, 24-5-12, 29-6-12 , 18-7-12)
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
microDoR Human
http://reprod.njmu.edu.cn/microdor/
Web based resource designed to determine whether mRNA degradation or translation repression occurs during the process of microRNA mediated gene silencing in Homo sapiens.
Lei Cheng ,Tao Zhou ; Xuejiang Guo ; Xiaofeng Song ; Xiaobai Zhang ; Ping Han ; Chen, Y.P. ; Jiahao Sha , microDoR for HUMAN: A web server to predict mode of miRNA-mediated gene silencing Bioinformatics and Biomedicine Workshops (BIBMW), 2010 IEEE International Conference on 18-18 Dec. 2010, On Page(s): 872 - 873
2010
100
microPIR
http://www4a.biotec.or.th/micropir/
Web based resource on promoter regions regulated by microRNAs in Homo sapiens.
Piriyapongsa J, Bootchai C, Ngamphiw C, Tongsima S. microPIR: An Integrated Database of MicroRNA Target Sites within Human Promoter Sequences. PLoS One. 2012;7(3):e33888. Epub 2012 Mar 16. PubMed PMID: 22439011; PubMed Central PMCID: PMC3306312.
2012
100
Only registered users can access the downloadable files.
microRNAbodymap
http://www.mirnabodymap.org/
Integrated database for functional analysis of microRNA in health and disease states.
Mestdagh P, Lefever S, Pattyn F, Ridzon D, Fredlund E, Fieuw A, Ongenaert M, Vermeulen J, De Paepe A, Wong L, Speleman F, Chen C, Vandesompele J. The microRNA body map: dissecting microRNA function through integrative genomics. Nucleic Acids Res. 2011 Nov 1;39(20):e136. Epub 2011 Aug 10. PubMed PMID: 21835775; PubMed Central PMCID: PMC3203610.
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
miRCancer
1. http://db.cs.ecu.edu/mirCancer/ 2. http://hdl.handle.net/10342/3195
Database on microRNA expression data in human cancers derived from experimental results.
Boya Xie, Robert Hochberg, Qin Ding and Di Wu, "MIRSAT & MIRCDB: An Integrated microRNA Sequence Analysis Tool and a Cancer-associated microRNA Database", International Conference on Bioinformatics and Computational Biology, Honolulu, Hawaii, 2010, pp. 159-164.
2010
100
mirCoX
http://wrenlab.org/mirCoX/.
This database of empirically established miRNA-mRNA transcriptional correlations help to corroborate experimental observations and could be used to help refine and validate miRNA target predictions.
Giles CB, Girija-Devi R, Dozmorov MG, Wren JD.Giles CB, Girija-Devi R, Dozmorov MG,Wren JD.mirCoX a database of miRNA-mRNA expression correlations derived from RNA-seq meta-analysis.BMC Bioinformatics. 2013;14 Suppl 14:S17. doi: 10.1186/1471-2105-14-S14-S17. PMID: 24267917
2013
100
miRDis
http://sbbi.unl.edu/miRDis/index.php.
miRDis outperforms other state-of-the-art tools in both detection and quantification of miRNA from either animal or plant sources.
Zhang H, Vieira Resende E Silva B, Cui J.miRDis- A Web tool for endogenous and exogenous microRNA discovery based on deep-miRNA detection. Brief Bioinform.2017 Jan 10.PMID: 28073746
2017
100
miREC
http://www.mirecdb.org .
miREC database holds information about miRNAs and genes deregulated in endometrial cancer, as well as target-regulator relationships between these genes and miRNAs.
Ulfenborg B, Jurcevic S, Lindlöf A, Klinga-Levan K, Olsson B.miREC: a database of miRNAs involved in the development of endometrial cancer. BMC Res Notes. 2015 Mar 28;8:104. doi: 10.1186/s13104-015-1052-9.PMID: 25889518
2015
100
miRmine
http://guanlab.ccmb.med.umich.edu/
Useful to determine expression values for each miRNA.
Panwar B,Omen GS,Guan Y.miRmine- A Database of Human miRNA expression profiles.Bioinformatics. 2017 Jan 19. .PMID: 28108447.
2017
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
miRNASong
http://www.med.muni.cz/histology/miRNAsong/.
It generates miRNA sponge constructs for specific miRNAs and miRNA families/clusters and tests them for potential binding to miRNAs in selected organisms.
Barta T, Peskova L, Hampl A. Sci Rep. miRNASong- a web based tool for generation of miRNA sponge and testing of constructs in silico.
2016
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
miRo
http://ferrolab.dmi.unict.it/miro
A web-based resource that describes the relationship between microRNAs and its expression in humans.
Lagana A, Forte S, Giudice A, Arena MR, Puglisi PL, Giugno R, Pulvirenti A, Shasha D, Ferro A. miRò: a miRNA knowledge base. Database (Oxford). 2009;2009:bap008. Epub 2009 Aug 4. PubMed PMID: 20157481; PubMed Central PMCID: PMC2794794
2009
100
miRPower
www.kmplot.com/mirpower
It perform a survival analysis for the identification and validation of prognostic miRNA markers in breast cancer.
Lánczky A, Nagy Á, Bottai G, Munkácsy G, Szabó A, Santarpia L, Gy?rffy B.miRpower: a web-tool to validate survival-associated miRNAs utilizing expression data from 2178 breast cancer patients.Breast Cancer Res Treat. 2016 Dec;160(3):439-446.PMID: 27744485.
2016
100
miRQuest
http://mirquest.integrativebioinformatics.me/.
It is an integration of different miRNA prediction tools for miRNA identification in a user-friendly environmentand comparison of these prediction tools.
Aguiar RR, Ambrosio LA, Sepúlveda-Hermosilla G, Maracaja-Coutinho V, Paschoal AR.miRQuest: integration of tools on a Web server for microRNA research. Genet Mol Res. 2016 Mar 28;15(1). doi: 10.4238/gmr.15016861. PMID:27050998
2016
100
MirSNP
http://cmbi.bjmu.edu.cn/mirsnp
MirSNP is a collection of human SNPs in predicted miRNA-mRNA binding sites.
Liu C, Zhang F, Li T, Lu M, Wang L, Yue W, Zhang D.Liu C, Zhang F, Li T, Lu M, Wang L, Yue W, Zhang D.BMC Genomics. 2012 Nov 23;13:661. doi: 10.1186/1471-2164-13-661.PMID: 23173617
2013
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
miRstart
http://mirstart.mbc.nctu.edu.tw/
Online resource of human microRNA TSSs (transcription start sites), determined from datasets of relevant TSS- based experiments .
Chien CH, Sun YM, Chang WC, Chiang-Hsieh PY, Lee TY, Tsai WC, Horng JT, Tsou AP, Huang HD. Identifying transcriptional start sites of human microRNAs based on high-throughput sequencing data. Nucleic Acids Res. 2011 Aug 5. [Epub ahead of print] PubMed PMID: 21821656.
2011
100
miRT
http://www.isical.ac.in/~bioinfo_miu/miRT/miRT.php
Resource on human microRNA transcription start sites.
Malay Bhattacharyya and Sanghamitra Bandyopadhyay, A Database for TSSs of Human MicroRNAs, doi:10.1038/npre.2012.6832.1, Nature precedings, Jan 2012
2012
100
miRvar
http://genome.igib.res.in/mirlovd
Database of curated genetic polymorphism in microRNA loci in the human genome.
Bhartiya D, Laddha SV, Mukhopadhyay A, Scaria V. miRvar: A comprehensive database for genomic variations in microRNAs. Hum Mutat. 2011 Jun;32(6):E2226-45. doi: 10.1002/humu.21482. Epub 2011 Feb 24. PubMed PMID: 21618345.
2011
100
Platform accessible for community curation endeavours.
miTRATA
https://wasabi.dbi.udel.edu/?apps/ta/.
Web tool that describe algorithm for 3? analysis of sRNAs , generating reports detailing the complexity of truncation and tailing modifications
Parth Patel, S. Deepthi, Ramachandruni, Atul Kakrana, Mayumi Nakano. miTRATA: a web-based tool for mi croRNA Tr uncation a nd T ailing A nalysis.Bioinformatics (2016) 32 (3): 450-452.PMID: 26454275
2016
100
Mpred
http://www.mir.mirworks.in/publications.html
Computational tool for determining human microRNAs using neural network and Hidden Markov Model.
Reshmi G.,Vinod Chandra S.S., Achuthsankar S. Nair, Oommen V. Ommen and M.Radhakrishna Pillai, Mpred: Computational prediction of human microRNAs using neural network and hidden Markov model, Proceedings of Asia Pacific Bioinformatics Conference-2010, Banglore, India, 18th - 21st January 2010.
2010
100
URL could not be retrieved 11-4-12, 22-4-12, 24-5-12, .29-6-12 , 18-7-12.
Mtar
http://www.mir.mirworks.in/mtar.html
In silico tool for identifying potential target sites (all 3 types) of human microRNAs.
Chandra V, Girijadevi R, Nair AS, Pillai SS, Pillai RM. MTar: a computational microRNA target prediction architecture for human transcriptome. BMC Bioinformatics. 2010 Jan 18;11 Suppl 1:S2. PubMed PMID: 20122191; PubMed Central PMCID: PMC3009490.
2010
100
Error message displayed after entering data for analysis. 18-7-12
Mtar
MTar identifies potential targets of 101 experimentally proved microRNAs.The performance of MTar was compared against existing solutions and the method is found to be more accurate.
Chandra V, Girijadevi R, Nair AS, Pillai SS, Pillai RM.MTar: A computational microRNA target prediction architecture for human transcriptome.BMC Bioinformatics. 2010 Jan 18;11 Suppl 1:S2. doi: 10.1186/1471-2105-11-S1-S2.PMID: 20122191
2010
100
OKCAM - Ontology-based Knowledgebase for Cell Adhesion Molecules
http://okcam.cbi.pku.edu.cn
A database on human based cell adhesion molecules with additional information on related microRNA.
Li CY, Liu QR, Zhang PW, Li XM, Wei L, Uhl GR. OKCAM: an ontology-based, human-centered knowledgebase for cell adhesion molecules. Nucleic Acids Res. 2009 Jan;37(Database issue):D251-60. Epub 2008 Sep 12. PubMed PMID: 18790807
2009
100
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
Patrocles
(http://www.patrocles.org/)
The Patrocles database compiles DNA sequence polymorphisms (DSPs) that are predicted to perturb miRNA-mediated gene regulation.
Hiard S, Charlier C, Coppieters W, Georges M, Baurain D.Patrocles: A database of polymorphic miRNA-mediated gene regulation in vertebrates.Nucleic Acids Res. 2010 Jan;38(Database issue):D640-51. doi: 10.1093/nar/gkp926. PMID: 19906729
2010
100
PD base
http://bioportal.kobic.re.kr/PDbase/
Web based resource on genes related to Parkinson's disease, including information on related microRNA.
Yang JO, Kim WY, Jeong SY, Oh JH, Jho S, Bhak J, Kim NS. PDbase: a database of Parkinson's disease-related genes and genetic variation using substantia nigra ESTs. BMC Genomics. 2009 Dec 3;10 Suppl 3:S32. PubMed PMID: 19958497; PubMed Central PMCID: PMC2788386.
2009
100
Psmir
http://www.bio-bigdata.com/Psmir/.
Psmir served as a valuable resource for dissecting the biological significance in small molecules' effects on miRNA expression, which will facilitate developing novel potential therapeutic targets or treatments for human cancers.
Not available
2016
100
PuTmiR
http://www.isical.ac.in/~bioinfo_miu/TF-miRNA1.php
Web server for analyzing the regulation of human microRNAs by transcription factors.
Bandyopadhyay S, Bhattacharyya M. PuTmiR: a database for extracting neighboring transcription factors of human microRNAs. BMC Bioinformatics. 2010 Apr 15;11:190. PubMed PMID: 20398296
2010
100
Dataset downloadable
PuTmiR
www.isical.ac.in/~bioinfo_miu/TF-miRNA.php
It provides an option for extracting the putative TFs for human miRNAs, as per the requirement of a user, based on genomic locality
Bandyopadhyay S, Bhattacharyya M.PuTmiR: A database for extracting neighboring transcription factors of human microRNAs. BMC Bioinformatics. 2010 Apr 15;11:190. doi: 10.1186/1471-2105-11-190.PMID: 20398296
2010
100
RBPDB- RNA-Binding Protein DataBase
http://rbpdb.ccbr.utoronto.ca/
The RNA-Binding Protein DataBase (RBPDB) predominantly contains experimentally derived information on RNA-binding sites, obtained by manual curation from primary literature sources.
Cook KB, Kazan H, Zuberi K, Morris Q, Hughes TR. RBPDB: a database of RNA-binding specificities. Nucleic Acids Res. 2011 Jan;39(Database issue):D301-8. Epub 2010 Oct 29. PubMed PMID: 21036867
2010
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
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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
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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
S-MED
http://www.oncomir.umn.edu/.
Sarcoma microRNA Expression Database (S-MED) is a repository that describes the patterns of miRNA expression in various human sarcoma types.S-MED provides both basic and advanced data search options for exploration of the data in heat map and text/numerical formats.The database also provides statistical details such as fold changes and P-values for differentially expressed miRNAs in each sarcoma type and corresponding normal tissue.
Sarver AL, Phalak R, Thayanithy V, Subramanian S.S-MED: sarcoma microRNA expression database. Lab Invest. 2010 May;90(5):753-61. doi: 10.1038/labinvest.2010.53.PMID: 20212452
2010
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S-MED- Sarcoma microRNA expression database
http://www.oncomir.umn.edu/
Sarcoma microRNA Expression Database (S-MED) is a compilation of specific features of miRNA expression in various types of human sarcoma.
Sarver AL, Phalak R, Thayanithy V, Subramanian S. S-MED: sarcoma microRNA expression database. Lab Invest. 2010 May;90(5):753-61. Epub 2010 Mar 8. PubMed PMID: 20212452.
2010
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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
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SSCprofiler
1. http://www.imbb.forth.gr/SSCprofiler.html 2. http://mirna.imbb.forth.gr/SSCprofiler
Computational tool for identification of novel microRNA genes.
Oulas A, Boutla A, Gkirtzou K, Reczko M, Kalantidis K, Poirazi P. Prediction of novel microRNA genes in cancer-associated genomic regions--a combined computational and experimental approach. Nucleic Acids Res. 2009 Jun;37(10):3276-87. Epub 2009 Mar 25. PubMed PMID: 19324892
2009
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StarMir
http://sfold.wadsworth.org
Bioinformatic tool for target identification of microRNAs including those that lack conserved sites, non-conserved human microRNAs, and poorly conserved viral mRNAs.
Long D, Chan CY, Ding Y. Analysis of microRNA-target interactions by a target structure based hybridization model. Pac Symp Biocomput. 2008:64-74. PubMed PMID: 18232104.
2008
100
Downloadable on request
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
YM500
http://ngs.ym.edu.tw/ym500/
It defines the criteria of isomiRs, and also integrates the information of dbSNP to help researchers distinguish isomiRs from SNPs.
Cheng WC, Chung IF, Huang TS, Chang ST, Sun HJ, Tsai CF, Liang ML, Wong TT, Wang HW.Nucleic Acids Res. 2013 Jan;41(Database issue):D285-94. doi: 10.1093/nar/gks1238.PMID: 23203880
2013
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