miRNA gene regulation resources

miRGen 2.0

Additional Info

  • Activitiy Active
  • Description
    DIANA-miRGen v3.0 provides the accurate cell-line-specific miRNA gene transcription start sites (TSSs), coupled with genome-wide maps of transcription factor (TF) binding sites in order to unveil the mechanisms of miRNA transcription regulation. To this end, more than 7.3 billion RNA-, ChIP- and DNase-Seq next generation sequencing reads were analyzed/assembled and combined with state-of-the-art miRNA TSS prediction and TF binding site identification algorithms.
  • Main feature Detection miRNAs and TF interactions
  • Unique features
    Search by miRNA or TF name
  • Organism Human, Mouse
  • Category miRNA gene regulation
  • Last observe Friday, 26 August 2016
  • Year published 2007
  • Citations per year 23.11
  • Last update Monday, 04 January 2016
  • Updated over past 3 years Yes
  • Relative Popularity 576459

CircuitsDB2

Additional Info

  • Activitiy Active
  • Description
    CircuitsDB 2 is an improvement and extension of our previous work, CircuitsDB, in which we systematically study, by computational means, the combined role of microRNAs and lncRNAs within the human regulatory network and their impact on cancer-related genes. CircuitsDB 2 contains a large number of regulatory circuits, composed by Transcription Factors, target genes, microRNAs and lincRNAs interacting together, in the human genome.
  • Main feature Containing miRNA-TF regulatory networks
  • Unique features
    Combined role of microRNAs and lncRNAs within the human regulatory network
    Regulatory circuits, composed by Transcription Factors, target genes, microRNAs and lncRNAs interacting together
  • Organism Human
  • Category miRNA gene regulation
  • Last observe Tuesday, 06 September 2016
  • Year published 2010
  • Citations per year 8.33
  • Last update Wednesday, 01 January 2014
  • Updated over past 3 years Yes
  • Relative Popularity 19312

miReg

Additional Info

  • Activitiy Active
  • Description
    miReg is a manually curated microRNA Regulation Resource that represents regulatory relationships among validated upstream regulators (Transcription factors or TFs, drugs, physical, and chemical), downstream targets, associated biological process, experimental condition or disease state, and up/down regulation of the miR in that condition in a graphical and user friendly manner along with corresponding published references.
  • Main feature Including regulatory interaction of TF and their targets
  • Unique features
    Containing validated upstream regulators as transcription factor, drug, physical, and chemical 
  • Organism Human, Mouse, Rat
  • Category miRNA gene regulation
  • Last observe Wednesday, 31 August 2016
  • Year published 2010
  • Citations per year 1
  • Last update Friday, 06 August 2010
  • Updated over past 3 years No
  • Relative Popularity 0

MIR@NT@N

Additional Info

  • Activitiy Inactive
  • Description
    MIR@NT@N is an effective computational approach to identify novel molecular regulations and to predict gene regulatory networks and sub-networks including conserved motifs within a given biological context. MIR@NT@N uses a graph-based approach to predict novel molecular actors across multiple regulatory processes (i.e. TFs acting on protein-coding or miRNA genes, or miRNAs acting on messenger RNAs). Exploiting these predictions, the user can generate networks and further analyze them to identify sub-networks, including motifs such as feedback and feedforward loops.
  • Main feature Containing TFs, genes and miRNAs and their interactions
  • Unique features
     Provides a user-friendly graph-based application connected to a large scale database
  • Organism Human, Mouse, Rat
  • Category miRNA gene regulation
  • Last observe Wednesday, 31 August 2016
  • Year published 2011
  • Citations per year 8.2
  • Last update Friday, 04 March 2011
  • Updated over past 3 years No
  • Relative Popularity 67612

miRStart

Additional Info

  • Activitiy Active
  • Description
    miRStart is a novel resource of human microRNA TSSs (transcription start sites), systematically incorporates significant datasets derived from TSS-relevant experiments to identify transcription start sites of microRNAs. The distribution patterns of these experimental features within 50 k upstream region of microRNA precursors provides an insight into determining reliable microRNA TSSs.
  • Main feature miRNA transcription start site (TSS)
  • Unique features
    Systematically incorporates datasets to identify transcription start sites of microRNAs
  • Organism Human
  • Category miRNA gene regulation
  • Last observe Friday, 02 September 2016
  • Year published 2011
  • Citations per year 14.4
  • Last update Wednesday, 06 July 2011
  • Updated over past 3 years No
  • Relative Popularity 23092

miRT

Additional Info

  • Activitiy Active
  • Description
    miRT is a novel database of validated miRNA TSSs prepared by collecting data from several experimental studies that validate miRNA TSSs and are available for full download. miRT is a web server and it is also possible to convert the TSS loci between different genome built. miRT might be a valuable resource for advanced research on miRNA regulation.
  • Main feature Validated TSS of human miRNAs
  • Unique features

    Search by miRNA name

  • Organism Human
  • Category miRNA gene regulation
  • Last observe Monday, 05 September 2016
  • Year published 2012
  • Citations per year 2.25
  • Last update Thursday, 23 August 2012
  • Updated over past 3 years No
  • Relative Popularity 122569

PmmR

Additional Info

  • Activitiy Active
  • Description
    PMMR constructed the miRNA and TF induced regulatory network for humans by combining all possible regulations between miRNAs and TFs. Topological analysis of the network revealed some of its non-trivial and intrinsic properties. The concept of topological overlap has been extended to formulate a novel dissimilarity measure that is capable of mining groups of closely interacting molecules from a weighted digraph such that the molecules in each group regulate each other to a large extent. Many of the identified TF modules are found to be enriched in different functional categories or displayed significant associations with common diseases.
  • Main feature Putative miRNA-miRNA regulations
  • Unique features
    Showing regulated and regulating miRNAs
  • Organism Human
  • Category miRNA gene regulation
  • Last observe Saturday, 03 September 2016
  • Year published 2011
  • Citations per year 1.4
  • Last update Wednesday, 23 March 2011
  • Updated over past 3 years No
  • Relative Popularity 122569

PuTmiR

Additional Info

  • Activitiy Active
  • Description
    PuTmiR provides an important resource for analyzing the direct and indirect regulation of human miRNAs. While it is already an established fact that miRNAs are regulated by TFs binding to their USR, this database might possibly help to study whether a miRNA can also be regulated by the TFs binding to their downstream region.
  • Main feature Putative TF-miRNA regulations
  • Unique features
    In 10 kb or custom regions
    Searching upstream or downstream reigons
  • Organism Human
  • Category miRNA gene regulation
  • Last observe Thursday, 01 September 2016
  • Year published 2010
  • Citations per year 4.67
  • Last update Thursday, 15 April 2010
  • Updated over past 3 years No
  • Relative Popularity 122569

RegRNA

Additional Info

  • Activitiy Active
  • Description
    RegRNA is an integrated web server for identifying the homologs of regulatory RNA motifs and elements against an input mRNA sequence. Both sequence homologs and structural homologs of regulatory RNA motifs can be recognized.
  • Main feature Regulatory RNA motifs and functional sites
  • Unique features
    Sequence homologs or structural homologs of regulatory RNA motifs can be identified
  • Organism Human
  • Category miRNA gene regulation
  • Last observe Saturday, 03 September 2016
  • Year published 2006
  • Citations per year 11.4
  • Last update Monday, 21 January 2013
  • Updated over past 3 years No
  • Relative Popularity 23092

TransmiR

Additional Info

  • Activitiy Active
  • Description
    TransmiR contains TFs and miRNAs with regulatory pairs between TFs and miRNAs. TransmiR included references to the published literature (PubMed ID) information about the organism in which the relationship was found, whether the TFs and miRNAs are involved with tumors, miRNA function annotation and miRNA-associated disease annotation. TransmiR provides a user-friendly interface by which interested parties can easily retrieve TF–miRNA regulatory pairs by searching for either a miRNA or a TF.
  • Main feature TF-miRNA regulations
  • Unique features
    Including 735 entries, which include 201 TFs, 209 miRNAs, 16 organisms

  • Organism Human
  • Category miRNA gene regulation
  • Last observe Monday, 29 August 2016
  • Year published 2009
  • Citations per year 22
  • Last update Wednesday, 30 January 2013
  • Updated over past 3 years No
  • Relative Popularity 0

RegRNA 2.0

Additional Info

  • Activitiy Active
  • Description
    RegRNA 2.0 is an integrated web server for identifying functional RNA motifs in an input RNA sequence. RegRNA 2.0 extends our previvous work, RegRNA which is a widely used regulatory RNA motifs identification tool by incoporating more analytical methods and updated data sources. Through our integrated user-friendly interface, user can conveniently use these analytical approaches and observe results with good graphical visualization.
  • Main feature Regulatory RNA motifs and functional sites
  • Unique features

    Functional RNA motifs in an input RNA sequence
    Observe results with good graphical visualization

  • Organism Human
  • Category miRNA gene regulation
  • Last observe Thursday, 01 September 2016
  • Year published 2013
  • Citations per year 13.33
  • Last update Monday, 21 January 2013
  • Updated over past 3 years No
  • Relative Popularity 23092

DIANA-mirExTra v2.0

Additional Info

  • Activitiy Active
  • Description
    DIANA-mirExTra v2.0 performs a combined DEA of mRNAs and microRNAs to uncover miRNAs and transcription factors (TFs) playing important regulatory roles between two investigated states. The web server uses as input miRNA/RNA-Seq read count data sets that can be uploaded for analysis. The web server utilizes miRNA:mRNA, TF:mRNA and TF:miRNA interactions derived from extensive experimental data sets.
  • Main feature Recognition of miRNAs and TF interactions
  • Unique features
    Containing miRNA:mRNA, TF:mRNA and TF:miRNA interactions derived from extensive experimental data sets
    Including 450 000 miRNA interactions and 2 000 000 TF binding sites from specific or high-throughput techniques
  • Organism Human, Mouse
  • Category miRNA gene regulation
  • Other covered categories
    miRNA expression
  • Last observe Wednesday, 31 August 2016
  • Year published 2010
  • Citations per year 9
  • Last update Monday, 20 June 2016
  • Updated over past 3 years Yes
  • Relative Popularity 2310477

EpimiR

Additional Info

  • Activitiy Active
  • Description
    EpimiR database collects 1974 regulations between 19 kinds of epigenetic modifications (such as DNA methylation, histone acetylation, H3K4me3, H3S10p) and 617 miRNAs across seven species (including Homo sapiens, Mus musculus, Rattus norvegicus, Gallus gallus, Epstein-Barr virus, Canis familiaris and Arabidopsis thaliana) from >300 references in the literature. These regulations can be divided into two parts: miR2Epi (103 entries describing how miRNA regulates epigenetic modification) and Epi2miR (1871 entries describing how epigenetic modification affects miRNA).
  • Main feature Regulation between miRNAs and epigenetic modifications
  • Unique features
    miRNA regulated by epigenetics
    miRNA regulating epigenetics
    Search by miRNA or epigenetics
  • Organism Human, Mouse, Other vertebrates, Rat
  • Category miRNA gene regulation
  • Last observe Friday, 26 August 2016
  • Year published 2014
  • Citations per year 3
  • Last update Monday, 10 June 2013
  • Updated over past 3 years No
  • Relative Popularity 0

microPIR2

Additional Info

  • Activitiy Active
  • Description
    microPIR2 provides approximately 80 million human and 40 million mouse predicted target sites. microPIR2 is a tool for comparative analysis of target sites on the promoters of human-mouse orthologous genes. In particular, this new feature was designed to identify potential microRNA-promoter interactions conserved between species that could be stronger candidates for further experimental validation. microPIR2 includes nuclear and cytoplasmic localization of microRNAs and miRNA-disease association.
  • Main feature MicroRNA target sites on promoter sequences
  • Unique features
    Search by gene, miRNA, disease or phenotype
  • Organism Human, Mouse
  • Category miRNA gene regulation
  • Last observe Monday, 29 August 2016
  • Year published 2012
  • Citations per year 4.25
  • Last update Tuesday, 04 November 2014
  • Updated over past 3 years Yes
  • Relative Popularity 614035

TMREC

Additional Info

  • Activitiy Active
  • Description
    TMREC integrated curated transcriptional and post-transcriptional regulations to construct the TF and miRNA regulatory network. Next, this database identified all linear paths using the Breadth First Search traversal method. Finally, we used known disease-related genes and miRNAs to measure the strength of association between cascades and diseases. Currently, TMREC consists of 74,248 cascades and 25,194 cascade clusters, involving in 412 TFs, 266 miRNAs and 545 diseases.
  • Main feature Transcription factor and miRNA regulatory cascades
  • Unique features
    Understand the transcriptional and post-transcriptional regulatory mechanisms in specific disease
    Identify the potential therapeutic targets in the upstream of the cascades
  • Organism Human
  • Category miRNA gene regulation
  • Last observe Monday, 29 August 2016
  • Year published 2015
  • Citations per year 2
  • Last update Thursday, 30 October 2014
  • Updated over past 3 years Yes
  • Relative Popularity 0