Composite target-prediction resource-tools

miRWalk 2.0

Additional Info

  • Activitiy Active
  • Description
    miRWalk2.0 is supplying the biggest available collection of predicted and experimentally verified miRNA-target interactions with various novel and unique features. miRWalk2.0 not only documents miRNA binding sites within the complete sequence of a gene, but also combines this information with a comparison of binding sites resulting from 12 existing miRNA-target prediction programs to build novel comparative platforms of binding sites for the promoter, cds, 5’- and 3’-UTR regions. It also documents experimentally verified miRNA-target interaction information collected via an automated text-mining search.
  • Main feature User-friendly composite target prediction resource
  • Unique features
    Combining miRNA target prediction results from DIANA-microT, miRanda, MirTarget2, RNAhybrid, PicTar4,  PicTar5, PITA, RNA22, TargetScan and  miRWalk
    Search of miRNA binding sites within 5´ UTR, CDS and 3´UTR
    Search in all or longer transcripts
    Predicted targets are diagrammed to pathways and diseases
  • Organism Human, Mouse, Rat
  • Category Composite target prediction
  • Other covered categories
    Experimentally validated miRNA targets
    miRNA expression
    miRNA roles in diseases
    miRNA interactions in pathways
  • Last observe Friday, 02 September 2016
  • Year published 2011
  • Citations per year 124.2
  • Last update Tuesday, 21 April 2015
  • Updated over past 3 years Yes
  • Relative Popularity 15843

HocTar

Additional Info

  • Activitiy Active
  • Description
    The HOCTAR (Host gene Opposite Correlated TARgets) tool is a new procedure to improve the prediction of miRNA targets. The HOCTAR procedure is based on the integration of expression profiling and sequence-based miRNA target recognition softwares. HOCTAR database is the first and unique database to use transcriptomic data to score putative miRNA targets looking at the expression behavior of their host genes, and it includes and re-analyzes all miRNA target predictions generated by softwares such as miRanda, TargetScan and PicTar. The HOCTAR contains the prediction target lists for 290 human intragenic miRNAs and also provides tentative assignments of miRNA function based on Gene Ontology analyses of their predicted targets.
  • Main feature Composite target prediction resource
  • Unique features
    Integrating miRNA target predictions of miRanda, TargetScan and PicTar
  • Organism Human
  • Category Composite target prediction
  • Other covered categories
    Target prediction correlated with expression data
  • Last observe Thursday, 01 September 2016
  • Year published 2011
  • Citations per year 3.8
  • Last update Wednesday, 13 October 2010
  • Updated over past 3 years No
  • Relative Popularity 1410127

mirDIP

Additional Info

  • Activitiy Active
  • Description
    mirDIP integrates prediction databases to elucidate accurate microRNA:target relationships. Pathway-based analysis of mirDIP data suggests microRNAs are involved in intra-pathway signalling. We identify two distinct classes of microRNAs, suggesting a hierarchical organization of microRNAs co-targeting genes both within and between pathways, and implying differential involvement of universe and intra-pathway microRNAs at the disease level.
  • Main feature Composite target prediction source
  • Unique features
    Merging microRNA predictions twelve microRNA prediction datasets  from DIANA-microT, microcosm, miRanda, PicTar, PITA, RNA22 and TargetScan algorithms  
    Finding signaling pathway-associated microRNAS
  • Organism Human
  • Category Composite target prediction
  • Other covered categories
    miRNA interactions in networks
  • Last observe Thursday, 01 September 2016
  • Year published 2011
  • Citations per year 15.4
  • Last update Monday, 01 August 2016
  • Updated over past 3 years Yes
  • Relative Popularity 4704

miRecords

Additional Info

  • Activitiy Active
  • Description
    miRecords is a resource for animal miRNA-target interactions. The Predicted Targets component of miRecords is an integration of predicted miRNA targets produced by 11 established miRNA target prediction programs. The Predicted Targets component of mIRecords integrates the predicted targets of DIANA-microT, MicroInspector, miRanda, MirTarget2, miTarget, NBmiRTar, PicTar, PITA, RNA22, RNAhybrid, and TargetScan/TargertScanS tools.
  • Main feature Composite target prediction source for nine species
  • Unique features
    Combining of predicted miRNA targets produced by 11  algorithms DIANA-microT, MicroInspector, miRanda, MirTarget2, miTarget, NBmiRTar, PicTar, PITA, RNA22, RNAhybrid and TargetScan
    Target predictions can be pooled with the validated interactions
  • Organism Human, Mouse, Other vertebrates, Insects, Nematodes, Rat
  • Category Composite target prediction
  • Other covered categories
    Experimentally validated miRNA targets
  • Last observe Monday, 29 August 2016
  • Year published 2009
  • Citations per year 82.86
  • Last update Saturday, 27 April 2013
  • Updated over past 3 years No
  • Relative Popularity 3131127

MiRGator v3.0

Additional Info

  • Activitiy Active
  • Description
    miRGator aims to be the microRNA (miRNA) portal encompassing microRNA diversity, expression profiles, target relationships, and various supporting tools.miRNA-mRNA target relations and expression correlations integrated for identifying reliable targets. We have merged 3 databases of validated targets and 6 databases of predicted targets. Inverse correlation of gene expression is a strong evidence of genuine targetedness, and we have specifically collected studies with miRNA and mRNA expression data from the same samples.
  • Main feature Composite target prediction source
  • Unique features
    Joining the results of PicTar, TargetScan, miRanda, microcosm, PITA and miRDB algorithms
    Containing microRNA diversity, expression profiles and target relationships
  • Organism Human
  • Category Composite target prediction
  • Other covered categories
    miRNA expression
    miRNA functions
    miRNA interactions in pathways
  • Last observe Friday, 26 August 2016
  • Year published 2013
  • Citations per year 11.3
  • Last update Tuesday, 01 January 2013
  • Updated over past 3 years No
  • Relative Popularity 5075541

miRNA body map

Additional Info

  • Activitiy Active
  • Description
    microRNA body map is an innovative approach to elucidate tissue-specific miRNA functions that goes beyond miRNA target prediction and expression correlation. This approach is based on a multi-level integration of corresponding miRNA and mRNA gene expression levels, miRNA target prediction, transcription factor target prediction and mechanistic models of gene network regulation. Predicted miRNA functions were either validated experimentally or compared to published data.
  • Main feature Composite target prediction resource
  • Unique features
    Integration of predicted miRNA targets produced by eight miRNA target algorithms  PITA, DIANA-microT, Microcosm, RNA22, TargetScan, miRDB, TarBase and mirecords
    miRNA function and their effect on pathways 
  • Organism Human, Mouse, Rat
  • Category Composite target prediction
  • Other covered categories
    miRNA expression
    miRNA function
  • Last observe Wednesday, 31 August 2016
  • Year published 2011
  • Citations per year 6
  • Last update Friday, 22 July 2011
  • Updated over past 3 years No
  • Relative Popularity 17407

miRNAMap 2.0

Additional Info

  • Activitiy Active
  • Description
    miRNAMap 2.0 collect experimental verified microRNAs and experimental verified miRNA target genes in human, mouse, rat, and other metazoan genomes. In addition to known miRNA targets, three computational tools previously developed, such as miRanda, RNAhybrid and TargetScan, were applied for identifying miRNA targets in 3' -UTR of genes. In order to reduce the false positive prediction of miRNA targets, several criteria are supported for filtering the putative miRNA targets.
  • Main feature Composite target prediction resource
  • Unique features
    Combining miRNA targeting results of Miranda, RNAHybrid and TargetScan algorithms
  • Organism Human
  • Category Composite target prediction
  • Other covered categories
    miRNA expression
  • Last observe Friday, 26 August 2016
  • Year published 2008
  • Citations per year 16.5
  • Last update Sunday, 01 July 2007
  • Updated over past 3 years No
  • Relative Popularity 23082

miRo v 2.0

Additional Info

  • Activitiy Active
  • Description
    miRò is a web-based knowledge base that provides users with miRNA-phenotype associations in humans. It integrates data from various online sources, such as databases of miRNAs, ontologies, diseases and targets, into a unified database equipped with an intuitive and flexible query interface and data mining facilities. The main goal of miRò analysis through sophisticated mining techniques and the introduction of a new layer of associations between genes and phenotypes inferred based on miRNAs annotations.
  • Main feature Composite target prediction resource
  • Unique features
    Integration miRNA target predictions of miRanda, PicTar, TargetScan and mirecords algorithms
  • Organism Human
  • Category Composite target prediction
  • Other covered categories
    miRNA function
    miRNA roles in diseases
  • Last observe Monday, 29 August 2016
  • Year published 2009
  • Citations per year 3.57
  • Last update Tuesday, 23 June 2009
  • Updated over past 3 years No
  • Relative Popularity 46488

mirRor Suite

Additional Info

  • Activitiy Active
  • Description
    miRror-Suite platform developed to yield a robust and concise explanation for miRNA regulation from a large collection of differentially expressed transcripts and miRNAs. Users select the preferred databases from 11 miRNA target prediction resources for predictions and numerous optional filters/parameters that restrict the search to the desired tissues, cell lines, level of expression and predictor scores.
  • Main feature Composite target prediction resource
  • Unique features
    Analyzing series of genes or miRNAs by integrating 11 miRNA target prediction resources
  • Organism Rat
  • Category Composite target prediction
  • Other covered categories
    miRNA interactions in pathways
    miRNA interactions in networks
  • Last observe Thursday, 01 September 2016
  • Year published 2010
  • Citations per year 4.5
  • Last update Wednesday, 23 April 2014
  • Updated over past 3 years Yes
  • Relative Popularity 29054

miRTar

 

 

Additional Info

  • Activitiy Active
  • Description
    MicroRNA Target prediction (miRTar) is a tool that enables biologists easily to identify the biological functions and regulatory relationships between a group of known/putative miRNAs and protein coding genes. It uses RNAHybrid, TargetScan, Miranda and PITA algorithms. It also provides perspective of information on the miRNA targets on alternatively spliced transcripts.
  • Main feature Predicting miRNA targets by integrating RNAhybrid,TargetScan, Miranda and PITA algorithms
  • Unique features
    Finding targets of a miRNAs based on miRNAs, genes or KEGG descriptions
    Present predictions of TargetScan, Miranda or verification of TarBase
    Conservation of target sites in different species
  • Organism Human
  • Category Composite target prediction
  • Other covered categories
    miRNA interactions in pathways
  • Last observe Thursday, 01 September 2016
  • Year published 2011
  • Citations per year 7
  • Last update Tuesday, 26 July 2011
  • Updated over past 3 years Yes
  • Relative Popularity 23092

BcmicrO

Additional Info

  • Activitiy Active
  • Description
    Since different existing algorithms rely on different features and classifiers, there is a poor agreement among the results of different algorithms. To benefit from the advantages of different algorithms, we proposed an algorithm called BCmicrO that combines the prediction of TargetScan, miRanda, PicTar, mirTarget, PITA, and DianamicroT.
  • Main feature Composite target prediction resource
  • Unique features
    Combines the prediction of TargetScan, miRanda, PicTar, mirTarget, PITA, and Diana microT
  • Organism Human
  • Category Composite target prediction
  • Last observe Monday, 29 August 2016
  • Year published 2012
  • Citations per year 0.25
  • Last update Monday, 17 December 2012
  • Updated over past 3 years No
  • Relative Popularity 26378

26378

Additional Info

  • Activitiy Active
  • Description
    ComiR (Combinatorial miRNA targeting) predicts whether a given mRNA is targeted by a set of miRNAs. ComiR uses miRNA expression to improve and combine multiple miRNA targets for each of the four prediction algorithms:miRanda, PITA, TargetScan and mirSVR. The composite scores of the four algorithms are then combined using a support vector machine trained on Drosophila Ago1 IP data.
  • Main feature Composite target prediction resource
  • Unique features
    Combining miRNA target prediction results from miRanda, PITA, TargetScan and mirSVR Using miRNA expression to improve and combine multiple miRNA targets
  • Organism Human, Mouse, Insects, Nematodes
  • Category Composite target prediction
  • Last observe Monday, 29 August 2016
  • Year published 2013
  • Citations per year 16.67
  • Last update Tuesday, 20 October 2015
  • Updated over past 3 years Yes
  • Relative Popularity 7995

miRGate

Additional Info

  • Activitiy Active
  • Description
    miRGate is a curated database of human, mouse and rat miRNAs/mRNAs targets. It is designed to analyze miRNA and gene isoforms lists under a common and consistent space of annotations. Including all existing 3 UTR and the entirely known miRNAs. All Havana biotypes and ENCODE principal isoforms for the three organisms are also included.
  • Main feature Composite target prediction resource
  • Unique features
    Using miRanda, Pita, RNAHybrid, Microtar, TargetScan, TarBase, mirTarBase and miRecords
    Analyze miRNA and gene isoforms lists under a common and consistent space of annotations
  • Organism Human, Mouse, Rat
  • Category Composite target prediction
  • Last observe Monday, 29 August 2016
  • Year published 2015
  • Citations per year 4
  • Last update Friday, 20 March 2015
  • Updated over past 3 years Yes
  • Relative Popularity 682038

miRSystem

Additional Info

  • Activitiy Active
  • Description
    miRSystem is a database which integrates seven well known miRNA target gene prediction programs: DIANA,miRanda, miRBridge, PicTar, PITA, rna22and TargetScan. This database contains validated data from TarBase and miRecords on interaction between miRNA and its target genes.
  • Main feature Composite target prediction resource
  • Unique features
    Combining miRNA targeting of DIANA, miRanda, miRBridge, PicTar, PITA, rna22 and TargetScan algorithms
  • Organism Human, Mouse
  • Category Composite target prediction
  • Last observe Wednesday, 31 August 2016
  • Year published 2012
  • Citations per year 11.5
  • Last update Friday, 13 May 2016
  • Updated over past 3 years Yes
  • Relative Popularity 6285

mirTarPri

Additional Info

  • Activitiy Active
  • Description
    mirTarPri is a web toolkit for prioritising candidate mirRNA targets in the context of functional genomic data. mirTarPri also provides a full prioritized mirRNA target list of six commonly used methods TargetScan, PicTar, PITA, DIANA-microT, miRanda and RNAhybrid
  • Main feature Composite target prediction based on functional genomic data
  • Unique features
    Prioritizing candidate mirRNA targets in the context of functional genomic data
    Using Gene Ontology and protein protein interaction networks
    Provides mirRNA target list of TargetScan, PicTar, PITA,DIANA-microT, miRanda, RNAhybrid tarBase, mirRecord and mir2Disease
  • Organism Human
  • Category Composite target prediction
  • Last observe Friday, 02 September 2016
  • Year published 2013
  • Citations per year 1.33
  • Last update Wednesday, 09 January 2013
  • Updated over past 3 years No
  • Relative Popularity 0

multiMiR

Additional Info

  • Activitiy Active
  • Description
    multiMiR is a comprehensive collection of predicted and validated miRNA-target interactions and their associations with diseases and drugs. multiMiR collecting nearly 50 million records from 14 different databases. User-defined cutoffs for predicted binding strength to provide the most confident selection.
  • Main feature Composite target prediction resource
  • Unique features
    Using predicted and validate miRNA-target Interactions
    Using DIANA-microT-CDS, ElMMo, MicroCosm, miRanda, miRDB, PicTar, PITA, TargetScan, miRecords, miRTarBase and TarBase algorithms
  • Organism Human, Mouse
  • Category Composite target prediction
  • Last observe Friday, 02 September 2016
  • Year published 2014
  • Citations per year 4.5
  • Last update Thursday, 24 July 2014
  • Updated over past 3 years Yes
  • Relative Popularity 19884

targetHub

Additional Info

  • Activitiy Active
  • Description
    targetHub is a database of miRNA-mRNA interactions. The interaction data is obtained various external data sources and in some cases computed in-house by algorithms implemented for miRNA target prediction
  • Main feature Composite target prediction resource
  • Unique features
    Using predicted and validate miRNA-target Interactions
    Using miRanda, PicTar4, PicTar5, TargetScan, miRecords and miRTarBase algorithms
  • Organism Human
  • Category Composite target prediction
  • Last observe Friday, 26 August 2016
  • Year published 2013
  • Citations per year 0.33
  • Last update Thursday, 29 August 2013
  • Updated over past 3 years No
  • Relative Popularity 28897

ToppMiR

Additional Info

  • Activitiy Active
  • Description
    ToppMiR is a web-based analytical workbench that allows miRs and mRNAs to be co-analyzed via biologically centered approaches in which gene function associated annotations are used to train a machine learning-based analysis engine. ToppMiR learns about biological contexts based on gene associated information from expression data or from a user-specified set of genes that relate to context-relevant knowledge or hypotheses.
  • Main feature Composite target prediction and ranking
  • Unique features
    Ranking targets based on biological functions and context
    Using PicTar, mirSVR, TargetScan, MSigDB, PITA, miRecords and miRTarbase algorithms
  • Organism Human
  • Category Composite target prediction
  • Last observe Saturday, 03 September 2016
  • Year published 2014
  • Citations per year 2.5
  • Last update Monday, 28 April 2014
  • Updated over past 3 years Yes
  • Relative Popularity 122953