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

MAGIA2

Additional Info

  • Activitiy Active
  • Description
    MAGIA2 is dedicated to the integrated analysis of in silico target prediction, microRNA (miRNA) and gene expression data for the reconstruction of post-transcriptional regulatory networks. MAGIA2 performs this integrative approach supporting different association measures, multiple organisms and almost all target predictions algorithms. MAGIA2 tries to dissect this complexity by reconstructing mixed regulatory circuits involving either miRNA or transcription factor (TF) as regulators.
  • Main feature Analyzing networks by considering effective regulators including miRNAs and TF
  • Unique features
    Integrate analysis of target prediction, miRNA and gene expression data to rebuild post-transcriptional regulatory networks
  • Organism Human, Mouse, Insects, Rat
  • Category miRNA interactions in networks
  • Last observe Thursday, 01 September 2016
  • Year published 2012
  • Citations per year 8
  • Last update Monday, 30 April 2012
  • Updated over past 3 years No
  • Relative Popularity 13697

MAGIA

Additional Info

  • Activitiy Active
  • Description
    MAGIA (miRNA and genes integrated analysis) is a novel web tool for the integrative analysis of target predictions, miRNA and gene expression data. MAGIA is divided into two parts: the query section allows the user to retrieve and browse updated miRNA target predictions computed with a number of different algorithms (PITA, miRanda and Target Scan) and Boolean combinations thereof. The analysis section comprises a multistep procedure for (i) direct integration through different functional measures of mRNA and miRNA expression data, (ii) construction of bipartite regulatory network of the best miRNA and mRNA putative interactions and (iii) retrieval of information available in several public databases of genes, miRNAs and diseases and via scientific literature text-mining.
  • Main feature Network analysis using target prediction and miRNA and gene expression profiles
  • Unique features
    Integrative analysis of target predictions, miRNA and gene expression data
    Using PITA, miRanda and Target Scan algorithms 
  • Organism Human
  • Category miRNA interactions in networks
  • Last observe Wednesday, 31 August 2016
  • Year published 2010
  • Citations per year 13
  • Last update Wednesday, 19 May 2010
  • Updated over past 3 years No
  • Relative Popularity 13697

FANTOM4 EdgeExpressDB

Additional Info

  • Activitiy Active
  • Description
    EdgeExpressDB is a novel database and set of interfaces for interpreting biological networks and comparing large high-throughput expression datasets that requires minimal development for new data types and search patterns. The FANTOM4 EdgeExpress database http://fantom.gsc.riken.jp/4/edgeexpress summarizes gene expression patterns in the context of alternative promoter structures and regulatory transcription factors and microRNAs using intuitive gene-centric and sub-network views. This is an important resource for gene regulation in acute myeloid leukemia, monocyte/macrophage differentiation and human transcriptional networks.
  • Main feature Biological network interpretation
  • Unique features
    Covering miRNAs, genes, promoters and expression profiles
  • Organism Human
  • Category miRNA interactions in networks
  • Last observe Friday, 02 September 2016
  • Year published 2009
  • Citations per year 4.86
  • Last update Sunday, 19 April 2009
  • Updated over past 3 years No
  • Relative Popularity 31214

mirConnX

Additional Info

  • Activitiy Inactive
  • Description
    mirConnX is a web interface for inferring, displaying and parsing mRNA and microRNA gene regulatory networks. mirConnX combines sequence information with gene expression data analysis to create a disease-specific, genome-wide regulatory network. A prior, static network has been constructed for all human and mouse genes. It consists of computationally predicted transcription factor (TF)-gene associations and miRNA target predictions. The prior network is supplemented with known interactions from the literature. Dynamic TF- and miRNA-gene associations are inferred from user-provided expression data using an association measure of choice. The static and dynamic networks are then combined using an integration function with user-specified weights.
  • Main feature mRNA and miRNA gene regulatory networks
  • Unique features
    Based on target predictions and computationally predicted TF-gene associations
  • Organism Human, Mouse
  • Category miRNA interactions in networks
  • Last observe Wednesday, 31 August 2016
  • Year published 2011
  • Citations per year 10.8
  • Last update Tuesday, 12 April 2011
  • Updated over past 3 years No
  • Relative Popularity 7947

mirDIP

Additional Info

  • Activitiy Active
  • Description
    "mirDIP integrates prediction databases to elucidate accurate microRNA:target relationships. Using NAViGaTOR to produce interaction networks implicating microRNAs in literature-based, KEGG-based and Reactome-based pathways, we find these signalling pathway networks have significantly more microRNA involvement compared to chance (p<0.05), suggesting microRNAs co-target many genes in a given pathway. Further examination of the micronome shows two distinct classes of microRNAs; universe microRNAs, which are involved in many signalling pathways; and intra-pathway microRNAs, which target multiple genes within one signalling pathway. 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 Network analysis by data integration
  • Unique features
    Integrating six miRNA prediction algorithms
  • Organism Human
  • Category miRNA interactions in networks
  • Last observe Wednesday, 31 August 2016
  • Year published 2011
  • Citations per year 15.4
  • Last update Friday, 25 February 2011
  • Updated over past 3 years No
  • Relative Popularity 4898

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 Network analysis of a series of genes or miRNAs
  • 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 networks
  • Other covered categories
    Composite target prediction
    miRNA interactions in pathways
  • 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

miRTrail

Additional Info

  • Activitiy Active
  • Description
    miRTrail is an integrative tool that allows for performing comprehensive analyses of interactions of genes and miRNAs based on expression profiles. The integrated analysis of mRNA and miRNA data should generate more robust and reliable results on deregulated pathogenic processes and may also offer novel insights into the regulatory interactions between miRNAs and genes. Our web-server excels in carrying out gene sets analysis, analysis of miRNA sets as well as the combination of both in a systems biology approach. To this end, miRTrail integrates information on 20.000 genes, almost 1.000 miRNAs, and roughly 280.000 putative interactions. For interactively visualizing obtained results, it relies on the network analyzers and viewers BiNA or Cytoscape-web, also enabling direct access to relevant literature.
  • Main feature Analyzing potential relationships between a set of miRNAs and mRNAs
  • Unique features
    Assess possible important implications of the miRNAs on the given disease
  • Organism Human, Mouse, Other vertebrates
  • Category miRNA interactions in networks
  • Last observe Wednesday, 31 August 2016
  • Year published 2012
  • Citations per year 4.25
  • Last update Wednesday, 22 February 2012
  • Updated over past 3 years No
  • Relative Popularity 212582

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

CoMeTa

Additional Info

  • Activitiy Active
  • Description
    Co-expression Meta-analysis of miRNA Targets (CoMeTa) procedure is based on the assumption that the targets of a given miRNA are likely to be co-expressed and therefore to belong to the same miRNA gene network. The CoMeTa tool aims at the inference of miRNA targets and miRNA-regulated gene networks by integrating expression data from hundreds of cellular and tissue conditions.
  • Main feature Identification of microRNA-regulated gene networks by target genes expression
  • Unique features
    Inferring miRNA targets and miRNA-regulated gene networks by integrating expression data from hundreds of cell and tissue conditions
    functional roles of the predicted miRNA regulated network
  • Organism Human
  • Category miRNA interactions in networks
  • Last observe Saturday, 03 September 2016
  • Year published 2012
  • Citations per year 15.75
  • Last update Sunday, 15 April 2012
  • Updated over past 3 years Yes
  • Relative Popularity 1134849