Resources of miRNA interactions in pathways

miRNApath

Additional Info

  • Activitiy Active
  • Description
    miRNApath is a database that uses miRNA target genes to link miRNAs to metabolic pathways. Currently, databases about miRNA target genes (DIANA miRGen), genomic maps (miRNAMap) and sequences (miRBase) do not provide such correlations. Additionally, miRNApath offers five search services and a download area. For each search, there is a specific type of input, which can be a list of target genes, miRNAs, or metabolic pathways, which results in different views, depending upon the input data, concerning relationships between the target genes, miRNAs and metabolic pathways.
  • Main feature Online resource utilizing miRNA target gene predictions to relate miRNAs to molecular pathways
  • Unique features
    Search by gene, miRNA or pathway name Based on target gene prediction
  • Organism Human, Mouse, Other vertebrates, Rat
  • Category miRNA interactions in pathways
  • Last observe Friday, 02 September 2016
  • Year published 2007
  • Citations per year 2.55
  • Last update Wednesday, 08 February 2006
  • Updated over past 3 years No
  • Relative Popularity 4092

DIANA_miRPath v3.0

Additional Info

  • Activitiy Active
  • Description
    DIANA-miRPath v3.0 is an online software suite dedicated to the assessment of miRNA regulatory roles and the identification of controlled pathways. DIANA-miRPath v3.0 database and functionality have been significantly extended to support all analyses for KEGG molecular pathways, as well as multiple slices of Gene Ontology (GO) in seven species. Importantly, more than 600 000 experimentally supported miRNA targets from DIANA-TarBase v7.0 have been incorporated into the new schema. Users of DIANA-miRPath v3.0 can harness this wealth of information and substitute or combine the available in silico predicted targets from DIANA-microT-CDS and/or TargetScan v6.2 with high quality experimentally supported interactions. A unique feature of DIANA-miRPath v3.0 is its redesigned Reverse Search module, which enables users to identify and visualize miRNAs significantly controlling selected pathways or belonging to specific GO categories based on in silico or experimental data.
  • Main feature Linking miRNAs to biologic pathways
  • Unique features
    Showing targeted genes on pathways
    Based on target prediction or experimentally validated results
    Using microT-CDS-v5.0, Tarbase-v7.0 or TargetScan algorithm
    Reverse Search, from pathway to miRNA
  • Organism Human, Mouse, Other vertebrates, Insects, Nematodes, Rat
  • Category miRNA interactions in pathways
  • Last observe Friday, 02 September 2016
  • Year published 2015
  • Citations per year 2
  • Last update Thursday, 14 May 2015
  • Updated over past 3 years Yes
  • Relative Popularity 114036

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. Researchers who performed large-scale transcriptomics or miRNA profiling experiments from cells and tissues will benefit from miRror-Suite. miRror-Suite provides a concise, plausible explanation for the regulation of miRNAs in such complex settings.
  • Main feature Connecting miRNAs to molecular pathways
  • Unique features
    Integrating 11 miRNA target prediction results
    Gene to miR or miR to Gene search
    Forward the results to external analysis
  • Organism Human, Mouse, Other vertebrates, Insects, Nematodes, Rat
  • Category miRNA interactions in pathways
  • Other covered categories
    Composite target prediction
    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

MiRGator v3.0

Additional Info

  • Activitiy Active
  • Description
    miRGator v3.0 compiled the deep sequencing miRNA data available in public and implemented several novel tools to facilitate exploration of massive data. miRNA–target relation is essential for understanding miRNA function and role in pathways. Coexpression analysis of miRNA and target mRNAs is visualized in the heat-map and network views where users can investigate the inverse correlation of gene expression and target relations, compiled from various databases of predicted and validated targets.
  • Main feature Identifying the miRNAs on various pathways
  • Unique features
    Using different algorithms for predicted effects
    Comparison a list of genes against defined gene sets such as KEGG pathway, Gene Ontology, the validated/predicted miRNA target databases and inversely coexpressed gene sets
  • Organism Human
  • Category miRNA interactions in pathways
  • Other covered categories
    Composite target prediction
    miRNA expression
    miRNA function
  • Last observe Friday, 26 August 2016
  • Year published 2013
  • Citations per year 11.33
  • Last update Thursday, 01 January 1970
  • Updated over past 3 years No
  • Relative Popularity 5075541

miRTar

Additional Info

  • Activitiy Active
  • Description
    miRTar adopts various analyzing scenarios to identify putative miRNA target sites of the gene transcripts and elucidates the biological functions of miRNAs toward their targets in biological pathways. The system has these features. Tthe prediction system is able to consider various analyzing scenarios. miRTar can analyze and highlight a group of miRNA-regulated genes that participate in particular KEGG pathways to elucidate the biological roles of miRNAs in biological pathways.
  • Main feature Relating miRNAs to various pathways
  • Unique features
    Based on integrating 4 miRNA prediction algorithms TargetScan, miRanda, PITA, and RNAHybrid
    Multiple scenarios for search
  • Organism Human
  • Category miRNA interactions in pathways
  • Other covered categories
    Composite target prediction
  • Last observe Thursday, 01 September 2016
  • Year published 2011
  • Citations per year 7
  • Last update Tuesday, 26 July 2011
  • Updated over past 3 years No
  • Relative Popularity 23092

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. It provides possible interactions between miRNAs and genes associated with 597 KEGG, 456 Panther and 522 Wiki pathways. users can also obtain miRNAs which are significantly enriched for their binding sites within the genes associated with pathways, ontologies and classes.
  • Main feature Determining miRNA impacts on pathways by miRNA targets
  • Unique features
    Based on predicted and validated miRNA targets
    Covering 375 pathways from three organisms
  • Organism Human, Mouse, Rat
  • Category miRNA interactions in pathways
  • Other covered categories
    Composite target prediction
    Experimentally validated miRNA targets
    miRNA expression
    miRNA roles in diseases
  • Last observe Thursday, 01 September 2016
  • Year published 2011
  • Citations per year 124.2
  • Last update Tuesday, 21 April 2015
  • Updated over past 3 years Yes
  • Relative Popularity 15864

miTALOS v2

Additional Info

  • Activitiy Active
  • Description
    miTALOS v2 is a tool that provides insights into tissue specific miRNA regulation of biological pathways. miTALOS v2 developed a novel methodology for tissue specific pathway analysis of miRNAs. This database incorporated the most recent and highest quality miRNA targeting data (TargetScan and StarBase), RNA-seq based gene expression data (EBI Expression Atlas) and multiple new pathway data sources to increase the biological relevance of the predicted miRNA-pathway associations.
  • Main feature miRNA-mediated regulation of signaling pathways
  • Unique features
    Analyzing the tissue-specific regulation of signaling pathways
  • Organism Human, Mouse
  • Category miRNA interactions in pathways
  • Other covered categories
    miRNA function
  • Last observe Thursday, 01 September 2016
  • Year published 2011
  • Citations per year 5.2
  • Last update Monday, 21 March 2016
  • Updated over past 3 years Yes
  • Relative Popularity 236828

DIANA_ miRPath v.2.0

Additional Info

  • Activitiy Active
  • Description
    DIANA-miRPath v2.0 utilize miRNA targets predicted with high accuracy based on DIANA-microT-CDS and/or experimentally verified targets from TarBase v6; combine results with merging and meta-analysis algorithms; perform hierarchical clustering of miRNAs and pathways based on their interaction levels; as well as elaborate sophisticated visualizations, such as dendrograms or miRNA versus pathway heat maps, from an intuitive and easy to use web interface. New modules enable DIANA-miRPath server to provide information regarding pathogenic single nucleotide polymorphisms (SNPs) in miRNA target sites (SNPs module) or to annotate all the predicted and experimentally validated miRNA targets in a selected molecular pathway (Reverse Search module).
  • Main feature Connecting miRNAs to pathways
  • Unique features

    Illustrating targeted genes on pathways 
    Based on target gene prediction 
    Using microT-CDS or TarBase 
    Reverse Search, from pathway to miRNA

  • Organism Human, Mouse, Insects, Nematodes
  • Category miRNA interactions in pathways
  • Last observe Thursday, 01 September 2016
  • Year published 2012
  • Citations per year 48.75
  • Last update Wednesday, 30 May 2012
  • Updated over past 3 years No
  • Relative Popularity 576459

miRSystem

Additional Info

  • Activitiy Active
  • Description
    miRSystem is a database which integrates seven well known miRNA target gene prediction programs and allows querying multiple miRNAs in one step for the associations between the miRNAs and their target genes. Two algorithms are incorporated to characterize the enriched biological functions/pathways among the genes targeting by queried miRNAs.
  • Main feature Relating miRNAs to molecular pathways
  • Unique features
    Target prediction based on DIANA, miRanda, miRBridge, PicTar, PITA, rna22 and TargetScan algorithms
    Enriched pathways of target genes are characterized by five pathway databases
  • Organism Human, Mouse
  • Category miRNA interactions in pathways
  • Last observe Saturday, 03 September 2016
  • Year published 2012
  • Citations per year 11.5
  • Last update Friday, 13 May 2016
  • Updated over past 3 years Yes
  • Relative Popularity 6304