| MiRrorhttp://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 |
|
| Genecopoeiahttp://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 | 97 |
|
| psRNATargethttp://plantgrn.noble.org/psRNATarget/ |
| Web based resource for plant small RNA target study and for use in high-throughput analysis of next generation sequencing data. |
| | Dai X, Zhao PX. psRNATarget: a plant small RNA target analysis server. Nucleic
Acids Res. 2011 Jul;39(Web Server issue):W155-9. Epub 2011 May 27. PubMed PMID:
21622958; PubMed Central PMCID: PMC3125753.
|
| 2011 | 97 |
|
| StarBasehttp://starbase.sysu.edu.cn/ |
| Web based resource to study microRNA- mRNA interaction network data obtained from Argonaute CLIP-Sequencing and Degradome-Sequencing experiments. |
| | Yang JH, Li JH, Shao P, Zhou H, Chen YQ, Qu LH. starBase: a database for
exploring microRNA-mRNA interaction maps from Argonaute CLIP-Seq and
Degradome-Seq data. Nucleic Acids Res. 2011 Jan;39(Database issue):D202-9. Epub
2010 Oct 30. PubMed PMID: 21037263 |
| 2011 | 98 |
|
| CLIPZhttp://www.clipz.unibas.ch/ |
| Web based resource and in silico analysis tool for experimentally derived target sites of RNA binding proteins. |
| | Khorshid M, Rodak C, Zavolan M. CLIPZ: a database and analysis environment for
experimentally determined binding sites of RNA-binding proteins. Nucleic Acids
Res. 2011 Jan;39(Database issue):D245-52. Epub 2010 Nov 17. PubMed PMID:
21087992M. |
| 2011 | 100 |
The user is required to register or login prior to uploading or analyzing data
The user is required to register or login prior to uploading or analyzing data |
| deepBasehttp://deepbase.sysu.edu.cn/ |
| A web-based resource to analyze deep sequencing data. |
| | Yang JH, Shao P, Zhou H, Chen YQ, Qu LH. deepBase: a database for deeply
annotating and mining deep sequencing data. Nucleic Acids Res. 2010
Jan;38(Database issue):D123-30. Epub 2009 Dec 4. PubMed PMID: 19966272; PubMed
Central PMCID: PMC2808990.
|
| 2010 | 100 |
|
| DSAP- Deep sequencing small RNA analysis pipelinehttp://dsap.cgu.edu.tw |
| Deep-Sequencing small RNA analysis pipeline (DSAP) is useful in interpretational studies of deep sequencing small RNA data sets from solexa sequencing platform. |
| | Huang PJ, Liu YC, Lee CC, Lin WC, Gan RR, Lyu PC, Tang P. DSAP:
deep-sequencing small RNA analysis pipeline. Nucleic Acids Res. 2010 Jul;38(Web
Server issue):W385-91. Epub 2010 May 16. PubMed PMID: 20478825; PubMed Central
PMCID: PMC2896168.
|
| 2010 | 100 |
|
| Ensemble_Calc1. http://mfold.rna.albany.edu/?q=DINAMelt/Ensemble-calc 2. http://mfold.rna.albany.edu/Ensemble |
| Assists in predicting the occurrence of microRNA:mRNA interaction at specified concentrations by computing the final concentrations of microRNA and mRNA and the net free energy change of interaction. |
| | Ragan C, Zuker M, Ragan MA. Quantitative prediction of miRNA-mRNA interaction
based on equilibrium concentrations. PLoS Comput Biol. 2011 Feb;7(2):e1001090.
Epub 2011 Feb 24. PubMed PMID: 21390282; PubMed Central PMCID: PMC3044769.
|
| 2011 | 100 |
|
| GeneCodishttp://genecodis.dacya.ucm.es |
| Bioinformatic resource to assist in the interpretational studies of high throughput experiments and functional interpretation of gene lists by integrating biological data from many sources. |
| | Nogales-Cadenas R, Carmona-Saez P, Vazquez M, Vicente C, Yang X, Tirado F,
Carazo JM, Pascual-Montano A. GeneCodis: interpreting gene lists through
enrichment analysis and integration of diverse biological information. Nucleic
Acids Res. 2009 Jul;37(Web Server issue):W317-22. Epub 2009 May 22. PubMed PMID:
19465387; PubMed Central PMCID: PMC2703901.
|
| 2007 | 100 |
The application is freely available.
The application is freely available. |
| GeneTrailhttp://genetrail.bioinf.uni-sb.de/tools.php |
| 1. Web based set of tools that assists a user in gene set functional enrichment analysis of highthroughput data. 2. An additional tool processes a given list of microRNAs and predicts their targeted genes in the format of their corresponding gene IDs. |
| | Backes, C., Keller, A., Kuentzer, J., Kneissl, B., Comtesse, N., Elnakady, Y.A., MFCller, R., Meese, E., and Lenhof, H.P. GeneTrail - advanced gene set enrichment analysis. Nucleic Acid Research, Web Server Issue 2007 |
| 2007 | 100 |
|
| Geoseqhttp://geoseq.mssm.edu |
| Tool for simplified analysis of deep-sequencing data (public sequencing datasets) . |
| | Gurtowski J, Cancio A, Shah H, Levovitz C, George A, Homann R, Sachidanandam
R. Geoseq: a tool for dissecting deep-sequencing datasets. BMC Bioinformatics.
2010 Oct 12;11:506. PubMed PMID: 20939882; PubMed Central PMCID: PMC2972303.
|
| 2010 | 100 |
|
| Lists2Networkshttp://www.lists2networks.org |
| Computational tool for use in the interpretational analysis of high-throughput experiments. |
| | Lachmann A, Ma'ayan A. Lists2Networks: integrated analysis of gene/protein
lists. BMC Bioinformatics. 2010 Feb 12;11:87. PubMed PMID: 20152038; PubMed
Central PMCID: PMC2843617.
|
| 2010 | 100 |
Requires registration prior to use and is free of cost.
Requires registration prior to use and is free of cost. |
| minRcos (Navon et al)http://bioinfo.cs.technion.ac.il/people/?zohar/RCoS/ |
| Software application to analyze microRNA expression data |
| | Navon R, Wang H, Steinfeld I, Tsalenko A, Ben-Dor A, Yakhini Z. Novel
Rank-based statistical methods reveal microRNAs with differential expression in
multiple cancer types. PLoS One. 2009 Nov 25;4(11):e8003. PubMed PMID: 19946373;
PubMed Central PMCID: PMC2777376.
|
| 2009 | 100 |
To be validated
To be validated |
| miRanalyzerhttp://bioinfo2.ugr.es/miRanalyzer/miRanalyzer.php |
| Web-based tool that enables interpretational studies of data acquired from deep sequencing experiments. |
| | Hackenberg M, Sturm M, Langenberger D, FalcF3n-P\E9rez JM, Aransay AM.
miRanalyzer: a microRNA detection and analysis tool for next-generation
sequencing experiments. Nucleic Acids Res. 2009 Jul;37(Web Server issue):W68-76.
Epub 2009 May 11. PubMed PMID: 19433510; PubMed Central PMCID: PMC2703919.
|
| 2009 | 100 |
|
| miRAS- miRNA Analysis Systemhttp://e-science.tsinghua.edu.cn/miras |
| miRNA Analysis System (miRAS) is a web-based tool for interpretational analysis of data obtained from microRNA expression studies such as total RNA clone method. |
| | Tian F, Zhang H, Zhang X, Song C, Xia Y, Wu Y, Liu X. miRAS: a data processing
system for miRNA expression profiling study. BMC Bioinformatics. 2007 Aug
4;8:285. PubMed PMID: 17683571; PubMed Central PMCID: PMC1963339.
|
| 2007 | 100 |
URL could not be retrieved on 30-3-12, 8-4-12, 22-4-12, 24-5-12, 29-6-12 , 18-7-12, 9-3-2017
URL could not be retrieved on 30-3-12, 8-4-12, 22-4-12, 24-5-12, 29-6-12 , 18-7-12, 9-3-2017 |
| miReducehttp://www.mdc-berlin.de/en/research/research_teams/systems_biology_of_gene_regulatory_elements/projects/mireduce/index.html |
| Computational tool used in experimental evaluation of genome wide mRNA log fold changes involving the knockout/ knockdown/ over-expression of single or many microRNAs.
|
| | Sood P, Krek A, Zavolan M, Macino G, Rajewsky N. Cell-type-specific signatures
of microRNAs on target mRNA expression. Proc Natl Acad Sci U S A. 2006 Feb
21;103(8):2746-51. Epub 2006 Feb 13. PubMed PMID: 16477010; PubMed Central PMCID:
PMC1413820. (tool name is not specifically mentioned in this article) |
| 2006 | 100 |
To be validated
To be validated |
| MIReNAhttp://www.ihes.fr/~carbone/data8/ |
| Computational tool for genome scale identification of precursor and mature microRNA and analysis of deep sequencing data. |
| | Mathelier A, Carbone A. MIReNA: finding microRNAs with high accuracy and no
learning at genome scale and from deep sequencing data. Bioinformatics. 2010 Sep
15;26(18):2226-34. Epub 2010 Jun 30. PubMed PMID: 20591903.
|
| 2010 | 100 |
To be validated
To be validated |
| mirExplorerhttp://biocenter.sysu.edu.cn/mir/ |
| Computational tool comprising of two modules: mirExplorer- genome and mirExplorer-NGS which are used for genome scale identification of microRNAs and next generation sequencing data respectively. |
| | Guan DG, Liao JY, Qu ZH, Zhang Y, Qu LH. mirExplorer: Detecting microRNAs from
genome and next generation sequencing data using the AdaBoost method with
transition probability matrix and combined features. RNA Biol. 2011 Sep 1;8(5).
[Epub ahead of print] PubMed PMID: 21881406.
|
| 2011 | 100 |
To be validated
To be validated |
| miRExpresshttp://miRExpress.mbc.nctu.edu.tw |
| Bioinformatic resource and tool for determining and analyzing microRNA expression profile from high-throughput sequencing records. |
| | Wang WC, Lin FM, Chang WC, Lin KY, Huang HD, Lin NS. miRExpress: analyzing
high-throughput sequencing data for profiling microRNA expression. BMC
Bioinformatics. 2009 Oct 12;10:328. PubMed PMID: 19821977; PubMed Central PMCID:
PMC2767369.
|
| 2009 | 100 |
To be validated
To be validated |
| mirKOhttp://www.knockoutmouse.org/martsearch |
| Mouse microRNA knockout resource is a collection of mutant embryonic stem cells harboring specific deletions for most of the microRNA genes reposited in miRBase. |
| | Prosser HM, Koike-Yusa H, Cooper JD, Law FC, Bradley A. A resource of vectors
and ES cells for targeted deletion of microRNAs in mice. Nat Biotechnol. 2011 Aug
7;29(9):840-5. doi: 10.1038/nbt.1929. PubMed PMID: 21822254; PubMed Central
PMCID: PMC3242032.
|
| 2011 | 100 |
|
| miRNAkeyhttp://ibis.tau.ac.il/miRNAkey |
| Software package designed for usage in the analysis of microRNA deep sequencing data. |
| | Ronen R, Gan I, Modai S, Sukacheov A, Dror G, Halperin E, Shomron N. miRNAkey:
a software for microRNA deep sequencing analysis. Bioinformatics. 2010 Oct
15;26(20):2615-6. Epub 2010 Aug 27. PubMed PMID: 20801911.
|
| 2010 | 100 |
To be validated
To be validated |
| miRonTophttp://www.microarray.fr:8080/miRonTop/index |
| A web-based tool that predicts the effect of microRNAs in a defined biological system based on results obtained from highthroughput sequencing or DNA microarrays. |
| | Le Brigand K, Robbe-Sermesant K, Mari B, Barbry P. MiRonTop: mining microRNAs
targets across large scale gene expression studies. Bioinformatics. 2010 Dec
15;26(24):3131-2. Epub 2010 Oct 19. PubMed PMID: 20959382; PubMed Central PMCID:
PMC2995122 |
| 2010 | 100 |
|
| mirTools1. http://centre.bioinformatics.zj.cn/mirtools/ 2. http://59.79.168.90/mirtools |
| Computational tool for determining potential novel microRNAs, profiling and analysis based on high throughput sequencing data. |
| | Zhu E, Zhao F, Xu G, Hou H, Zhou L, Li X, Sun Z, Wu J. mirTools: microRNA
profiling and discovery based on high-throughput sequencing. Nucleic Acids Res.
2010 Jul;38(Web Server issue):W392-7. Epub 2010 May 16. PubMed PMID: 20478827;
PubMed Central PMCID: PMC2896132.
|
| 2010 | 100 |
To be validated
To be validated |
| miRTrailhttp://mirtrail.bioinf.uni-sb.de |
| miRTrail is stated to contain information on 20.000 genes, around 1.000 miRNAs, and approximately 280.000 putative interactions and can be applied to analyze microarray based expression profiles and NGS-based transcriptomic data. |
| | Laczny C, Leidinger P, Haas J, Ludwig N, Backes C, Gerasch A, Kaufmann M, Vogel B, Katus HA, Meder B, Stahler C, Meese E, Lenhof HP, Keller A. miRTrail - a comprehensive webserver for analyzing gene and miRNA patterns to enhance the understanding of regulatory mechanisms in diseases. BMC Bioinformatics. 2012 Feb 22;13(1):36. [Epub ahead of print] PubMed PMID: 22356618. |
| 2012 | 100 |
|
| miRTRAPhttp://flybuzz.berkeley.edu/miRTRAP.html |
| In silico tool for processing high throughput sequencing data and identification of microRNAs. |
| | Hendrix D, Levine M, Shi W. miRTRAP, a computational method for the systematic
identification of miRNAs from high throughput sequencing data. Genome Biol.
2010;11(4):R39. Epub 2010 Apr 6. PubMed PMID: 20370911; PubMed Central PMCID:
PMC2884542.
|
| 2010 | 100 |
To be validated
To be validated |
| SigTermshttp://sigterms.sourceforge.net |
| A desktop software application which is designed to display all microRNA:mRNA functional units based on an experimentally derived set of genes for a chosen target prediction database. |
| | Creighton CJ, Nagaraja AK, Hanash SM, Matzuk MM, Gunaratne PH. A
bioinformatics tool for linking gene expression profiling results with public
databases of microRNA target predictions. RNA. 2008 Nov;14(11):2290-6. Epub 2008
Sep 23. PubMed PMID: 18812437
|
| 2008 | 100 |
To be validated
To be validated |
| Sylamerhttp://www.ebi.ac.uk/enright/sylamer/ |
| Computational tool to assess the effect of microRNA/ siRNA (including off-targets) from expression data derived from RNA interference experiments, microRNA knockout studies etc. |
| | van Dongen S, Abreu-Goodger C, Enright AJ. Detecting microRNA binding and
siRNA off-target effects from expression data. Nat Methods. 2008
Dec;5(12):1023-5. Epub 2008 Nov 2. PubMed PMID: 18978784; PubMed Central PMCID:
PMC2635553.
|
| 2008 | 100 |
|
| Sylarrayhttp://www.ebi.ac.uk/enright/sylarray |
| Online resource for interpretational studies of small RNA (miRNA, siRNA) effects from large-scale expression datasets. |
| | Bartonicek N, Enright AJ. SylArray: a web server for automated detection of
miRNA effects from expression data. Bioinformatics. 2010 Nov 15;26(22):2900-1.
Epub 2010 Sep 24. PubMed PMID: 20871108.
|
| 2010 | 100 |
|
| TargetRankhttp://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
Dataset downloadable |
| XIP-seq PlatformURL not found |
| Integrative computational tool designed for analysis of high throughput sequencing data. |
| | Xin Wang; Mingxiang Teng; Guohua Wang; Yuming Zhao; Xu Han; Weixing Feng; Lang Li; Sanford, J.; Yunlong Liu; xIP-seq Platform: An Integrative Framework for High-Throughput Sequencing Data Analysis, Bioinformatics, 2009. OCCBIO '09. Ohio Collaborative Conference on Issue Date: 15-17 June 2009 On page(s): 26 - 31
|
| 2009 | 100 |
|
