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A comparative account of microRNA resources, feature-validations and application-based categorizations : DISEASE/ TISSUE SPECIFIC
Resources Important features / utilities*CitationsYear of publicationRank by usage frequency Click to Edit / Add comments
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.
MiRror
http://www.proto.cs.huji.ac.il/mirror
Bioinformatic resource that incorporates predictions from several microRNA resources and is useful for analyzing output data from large scale studies such as microRNA profiling, proteomics and gene expression arrays.
Friedman Y, Naamati G, Linial M. MiRror: a combinatorial analysis web tool for ensembles of microRNAs and their targets. Bioinformatics. 2010 Aug 1;26(15):1920-1. Epub 2010 Jun 6. PubMed PMID: 20529892.
2010
96
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
CAMi-Finder
http://www.isical.ac.in/~bioinfo_miu/web_isi.html
Web-based resource developed to provide information on microRNAs known to be related to cancer.
Not available
Not available
100
Can download validated cancer-miRNA information.
CircInteractome
http://circinteractome.nia.nih.gov
Not available
2016
100
dbDEMC- Database of differentially expressed miRNAs
http://159.226.118.44/dbDEMC/index.html
Web-based resource on cancer related microRNAs.
Yang Z, Ren F, Liu C, He S, Sun G, Gao Q, Yao L, Zhang Y, Miao R, Cao Y, Zhao Y, Zhong Y, Zhao H. dbDEMC: a database of differentially expressed miRNAs in human cancers. BMC Genomics. 2010 Dec 2;11 Suppl 4:S5. PubMed PMID: 21143814; PubMed Central PMCID: PMC3005935.
2010
100
Datasets downloadable.
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
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
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.
GeneHub-GEPIS
1. http://research-public.gene.com/ 2.http://research-public.gene.com/Research/genentech/genehub-gepis/index.html 3. http://www.cgl.ucsf.edu/Research/genentech/genehub-gepis/
GeneHub-GEPIS is a bioinformatic tool for inferring gene expression patterns in a large panel of normal and cancer tissues based on human and mouse EST sequence abundance.
Zhang Y, Luoh SM, Hon LS, Baertsch R, Wood WI, Zhang Z. GeneHub-GEPIS: digital expression profiling for normal and cancer tissues based on an integrated gene database. Nucleic Acids Res. 2007 Jul;35(Web Server issue):W152-8. Epub 2007 Jun 1. PubMed PMID: 17545196
2007
100
Datasets downloadable
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.
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
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
mimiRNA
1. http://mimirna.centenary.org.au/mep/formulaire.html 2. http://mimirna.centenary.org.au
Resource to explore expression status and functional association between microRNAs and their targets
Ritchie W, Flamant S, Rasko JE. mimiRNA: a microRNA expression profiler and classification resource designed to identify functional correlations between microRNAs and their targets. Bioinformatics. 2010 Jan 15;26(2):223-7. Epub 2009 Nov 17. PubMed PMID: 19933167.
2010
100
Dataset downloadable
MIRAGAA
http://www.csse.unimelb.edu.au/~rgaire/MIRAGAA/index.html
Computational approach to study the association of genomic variations in cancer and consequent variation in microRNA expression.
Gaire RK, Bailey J, Bearfoot J, Campbell IG, Stuckey PJ, Haviv I. MIRAGAA--a methodology for finding coordinated effects of microRNA expression changes and genome aberrations in cancer. Bioinformatics. 2010 Jan 15;26(2):161-7. Epub 2009 Nov 23. PubMed PMID: 19933823.
2010
100
To be validated
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
miRdSNP
http://mirdsnp.ccr.buffalo.edu
Web-based resource that facilitates the study of disease related SNPs and their potential effects on 3'UTR associated target sites of human microRNAs.
Bruno AE, Li L, Kalabus JL, Pan Y, Yu A, Hu Z. miRdSNP: a database of disease-associated SNPs and microRNA target sites on 3'UTRs of human genes. BMC Genomics. 2012 Jan 25;13:44. PubMed PMID: 22276777; PubMed Central PMCID: PMC3287127.
2012
100
Dataset downloadable
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
miRGator, miRGator v2.0
1. http://genome.ewha.ac.kr/miRGator/ 2. http://miRGator.kobic.re.kr 3. http://mirgator.kobic.re.kr:8080/MEXWebApp/
An integrated database for functional annotation of microRNA that includes expression, regulation, function, pathway,pathological or disease terms as well as microRNA targeting (miRanda, picTar and TargetScan).
Nam S, Kim B, Shin S, Lee S. miRGator: an integrated system for functional annotation of microRNAs. Nucleic Acids Res. 2008 Jan;36(Database issue):D159-64. Epub 2007 Oct 16. PubMed PMID: 17942429
2008
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 ).
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
miRNeye
http://mirneye.tigem.it/
Mouse eye atlas depicting the expression pattern and location of 221 microRNAs in developing and adult mouse
Karali M, Peluso I, Gennarino VA, Bilio M, Verde R, Lago G, Dollé P, Banfi S. miRNeye: a microRNA expression atlas of the mouse eye. BMC Genomics. 2010 Dec 20;11:715. PubMed PMID: 21171988; PubMed Central PMCID: PMC3018480.
2010
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
MISIM
http://cmbi.bjmu.edu.cn/misim
Computational tool for measuring microRNA functional similarity for a given microRNA list and generating a microRNA functional network in the context of microRNA related diseases.
Wang D, Wang J, Lu M, Song F, Cui Q. Inferring the human microRNA functional similarity and functional network based on microRNA-associated diseases. Bioinformatics. 2010 Jul 1;26(13):1644-50. Epub 2010 May 3. PubMed PMID: 20439255.
2010
100
Dataset downloadable
MMIA- MicroRNA and mRNA integrated analysis
1. http://129.79.244.122/~MMIA/mmia_main.html 2. http://cancer.informatics.indiana.edu/mmia
Computational tool for analyzing biological functions of microRNA expression by combining microRNA and mRNA expression data with computationally identified microRNA target information from TargetScan, PITA and PicTar.
Nam S, Li M, Choi K, Balch C, Kim S, Nephew KP. MicroRNA and mRNA integrated analysis (MMIA): a web tool for examining biological functions of microRNA expression. Nucleic Acids Res. 2009 Jul;37(Web Server issue):W356-62. Epub 2009 May 6. PubMed PMID: 19420067; PubMed Central PMCID: PMC2703907.
2009
100
mrSNP
http://mrsnp.osu.edu.
mrSNP is a highly adaptable and performing tool for predicting the effect a 3’UTR SNP will have on miRNA binding.
Deveci M, Catalyürek UV, Toland AE.mrSNP: software to detect SNP effects on microRNA mrSNP: software to detect SNP effects on microRNA binding.BMC Bioinformatics. 2014 Mar 15;15:73. doi: 10.1186/1471-2105-15-73.PMID: 24629096
2014
100
Musmirus
http://www.kimmelcancercenter.org/siracusa/musmirsus.htm
Musmirus database was developed to compare the location of microRNA genes with the location of solid tumor susceptibility and modifier loci in the mouse.
Not available
Not available
100
The MUSMIRSUS database is maintained by Dr. Linda D. Siracusa, Dr. Cinzia Sevignani, and Stephanie Nnadi at Thomas Jefferson University, 233 South 10th Street, Philadelphia, PA 19107.
ncRNAppi database
http://ncrnappi.cs.nthu.edu.tw
Database on pathologically altered microRNA target pathways.
Ng KL, Liu HC, Lee SC. ncRNAppi--a tool for identifying disease-related miRNA and siRNA targeting pathways. Bioinformatics. 2009 Dec 1;25(23):3199-201. Epub 2009 Oct 6. PubMed PMID: 19808883.
2009
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
PhenoMir
http://mips.helmholtz-muenchen.de/phenomir
Web based resource on altered microRNA function in disease and physiological processes.
Ruepp A, Kowarsch A, Schmidl D, Buggenthin F, Brauner B, Dunger I, Fobo G, Frishman G, Montrone C, Theis FJ. PhenomiR: a knowledgebase for microRNA expression in diseases and biological processes. Genome Biol. 2010 Jan 20;11(1):R6. PubMed PMID: 20089154
2010
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
Seqbuster
1. http://davinci.crg.es/estivill_lab/seqbuster/index.php?option=com_content&view=article&id=63:download-version-20&catid=43:seqbuster-20&Itemid=53 2. http://estivill_lab.crg.es/seqbuster.
In silico tool for analysis of small RNA datasets such that It may assist in finding significant variants of microRNA in normal or diseased states.
Pantano L, Estivill X, Martí E. SeqBuster, a bioinformatic tool for the processing and analysis of small RNAs datasets, reveals ubiquitous miRNA modifications in human embryonic cells. Nucleic Acids Res. 2010 Mar;38(5):e34. Epub 2009 Dec 11. PubMed PMID: 20008100; PubMed Central PMCID: PMC2836562.
2010
100
The software and Excel VBA source code are freely available. To be validated.
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
100
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
100
TFmiR
http://service.bioinformatik.uni-saarland.de/tfmir.
TFmiR provides an extended downstream analysis, a variety of user parameters, user input scenarios and incorporates information from various well-established regulatory databases.
Hamed M, Spaniol C, Nazarieh M, Helms V.TFmiR: a web server for constructing and analyzing disease-specific transcription factor and miRNA co-regulatory networks.Nucleic Acids Res. 2015 Jul 1;43(W1):W283-8. doi: 10.1093/nar/gkv418.PMID: 25943543
2015
100
TMREC
http://bioinfo.hrbmu.edu.cn/TMREC/.
TMREC is a public database for the retrieval and visualisation of TFs and miRNAs regulatory cascades in human diseases.
Wang S, Li W, Lian B, Liu X, Zhang Y, Dai E, Yu X, Meng F, Jiang W, Li X.TMREC: A Database of Transcription Factor and MiRNA Regulatory Cascades in Human Diseases. PLoS One. 2015 May 1;10(5):e0125222.doi: 10.1371/journal.pone.0125222.PMID: 25932650
2015
100
ViTa
http://vita.mbc.nctu.edu.tw/
Online resource comprising of virus data retrieved from databases such as miRBase, ICTV, VirGen, VBRC, and miRNAMap. Provides access to several tools to study microRNA and virus interaction.
Hsu PW, Lin LZ, Hsu SD, Hsu JB, Huang HD. ViTa: prediction of host microRNAs targets on viruses. Nucleic Acids Res. 2007 Jan;35(Database issue):D381-5. Epub 2006 Dec 5. PubMed PMID: 17148483
2007
100
 
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