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Total resources - 30
A comparative account of microRNA resources, feature-validations and application-based categorizations : EXPERIMENTAL data analysis
Resources Important features / utilities*CitationsYear of publicationRank by usage frequency Click to Edit / Add comments
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
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
psRNATarget
http://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
StarBase
http://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
CLIPZ
http://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
deepBase
http://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 pipeline
http://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_Calc
1. 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
GeneCodis
http://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.
GeneTrail
http://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., Müller, R., Meese, E., and Lenhof, H.P. GeneTrail - advanced gene set enrichment analysis. Nucleic Acid Research, Web Server Issue 2007
2007
100
Geoseq
http://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
Lists2Networks
http://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.
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
miRanalyzer
http://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, Falcón-Pérez 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 System
http://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
miReduce
http://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
MIReNA
http://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
mirExplorer
http://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
miRExpress
http://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
mirKO
http://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
miRNAkey
http://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
miRonTop
http://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
mirTools
1. 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
miRTrail
http://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
miRTRAP
http://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
SigTerms
http://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
Sylamer
http://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
Sylarray
http://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
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
XIP-seq Platform
URL 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
 
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