miRNA expression resources

mimiRNA

Additional Info

  • Activitiy Active
  • Description
    mimiRNA integrates expression data from 1483 samples and permits visualization of the expression of 635 human miRNAs across 188 different tissues or cell types. mimiRNA incorporates a novel sample classification algorithm, ExParser, that groups identical miRNA or mRNA experiments from separate sources. mimiRNA incorporates a decision tree algorithm to discover distinguishing miRNA features between two tissue or cell types.
  • Main feature Expression profiles of various organs and cell lines
  • Unique features
    Presenting and comparing miRNA expression profiles of different tissues or cell lines
    The expression profile of all microRNAs in a tissue or cell type and profile of a microRNA across all tissue and cell types
  • Organism Human
  • Category miRNA expression
  • Other covered categories
    Target prediction correlated with expression data
  • Last observe Thursday, 01 September 2016
  • Year published 2010
  • Citations per year 7.5
  • Last update Friday, 13 November 2009
  • Updated over past 3 years No
  • Relative Popularity 1077597

miRWalk

Additional Info

  • Activitiy Active
  • Description
    miRWalk is a comprehensive database that provides information on miRNA from Human, Mouse and Rat on their predicted as well as validated binding sites on their target genes. . It contains expression profiles of various organs and cell lines and several cell lines and organs connected to miRNA studies.
  • Main feature Expression profiles of various organs and cell lines
  • Unique features
    121 cell lines linked to miRNA investigations
    556 organs connected to miRNA studies
  • Organism Human, Mouse, Rat
  • Category miRNA expression
  • Other covered categories
    Composite target prediction
    Experimentally validated miRNA targets
    miRNA roles in diseases
    miRNA interactions in pathways
  • 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 15843

microRNA.org

Additional Info

  • Activitiy Active
  • Description
    MicroRNA.org is a comprehensive resource of microRNA target predictions and expression profiles. MicroRNA expression profiles are derived from a comprehensive sequencing project of a large set of mammalian tissues and cell lines of normal and disease origin. A user can explore microRNA expression profiles in various tissues.
  • Main feature Expression profiles of various tissues
  • Unique features
    Including expression profile of different miRNAs in various tissues and cancers
    Viewing multiple tissues in one search page
  • Organism Human, Mouse, Rat
  • Category miRNA expression
  • Other covered categories
    Single resource target prediction
  • Last observe Thursday, 01 September 2016
  • Year published 2008
  • Citations per year 122.75
  • Last update Monday, 01 November 2010
  • Updated over past 3 years No
  • Relative Popularity 638003

microTranspoGene

Additional Info

  • Activitiy Active
  • Description
    microTranspoGene is a database of human, mouse, zebrafish and nematode Transposed elements (TE)-derived microRNAs. Transposed elements (TEs) are mobile genetic sequences. During the evolution of eukaryotes TEs were inserted into active protein-coding genes, affecting gene structure, expression and splicing patterns, and protein sequences. Genomic insertions of TEs also led to creation and expression of new functional non-coding RNAs such as microRNAs.
  • Main feature Recognizing the effect of transposed elements on miRNA biogenesis
  • Unique features
    MicroRNAs which are derived from transposable elements (TEs) either transcriptionally or structurally
  • Organism Human, Mouse, Other vertebrates, Nematodes
  • Category miRNA expression
  • Last observe Thursday, 01 September 2016
  • Year published 2008
  • Citations per year 4.75
  • Last update Wednesday, 01 August 2007
  • Updated over past 3 years No
  • Relative Popularity 22430

miREnvironment

Additional Info

  • Activitiy Active
  • Description
    miREnvironment database contains a comprehensive collection and curation of experimentally supported interactions among miRNAs, environmental factors and phenotypes. The names of miRNAs, phenotypes, environmental factors, conditions of environmental factors, samples, species, evidence and references were further annotated. miREnvironment represents a biomedical resource for researches on miRNAs, environmental factors and diseases.
  • Main feature Identification of the relationship between miRNAs and environmental factors
  • Unique features
    miREnvironment integrated >2500 entries including 800 miRNAs, 260 experimental factors, 180 phenotypes from 17 species
  • Organism Human, Mouse, Rat
  • Category miRNA expression
  • Last observe Wednesday, 31 August 2016
  • Year published 2011
  • Citations per year 6
  • Last update Sunday, 09 September 2012
  • Updated over past 3 years No
  • Relative Popularity 0

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 catalogues and Expression profiles in various diseases, organs, and tissues based on deep sequencing data, which would provide an unbiased catalog of miRNA repertoire and accurate estimation of abundance. We also provide the list of differentially expressed miRNAs where normal samples are available.
  • Main feature Expression profile of miRNAs in tissues, organs and cell lines
  • Unique features
    Expression profile of tissues, organs and cell lines
    Including deep sequencing data as principal resources on microRNA diversity and expression
  • Organism Human
  • Category miRNA expression
  • Other covered categories
    Composite target prediction
    miRNA functions
    miRNA interactions in pathways
  • Last observe Friday, 26 August 2016
  • Year published 2013
  • Citations per year 11.33
  • Last update Tuesday, 01 January 2013
  • Updated over past 3 years No
  • Relative Popularity 5075541

miROrtho

Additional Info

  • Activitiy Active
  • Description

    The miROrtho database presents the results of a comprehensive computational survey of miRNA gene candidates across the majority of sequenced metazoan genomes. This database was designed and applied a three-tier analysis pipeline: (i) an SVM-based ab initio screen for potent hairpins, plus homologs of known miRNAs, (ii) an orthology delineation procedure and (iii) an SVM-based classifier of the ortholog multiple sequence alignments. The web interface provides direct access to putative miRNA annotations, ortholog multiple alignments, RNA secondary structure conservation, and sequence data.

  • Main feature Expression data of miRNAs
  • Unique features

    Both known and predicted miRNAs

  • Organism Human, Mouse, Other vertebrates, Insects, Viruses, Nematodes, Plants, Rat
  • Category miRNA expression
  • Other covered categories

    miRNA sequence and annotation

  • Last observe Wednesday, 31 August 2016
  • Year published 2009
  • Citations per year 5.86
  • Last update Thursday, 01 January 2009
  • Updated over past 3 years Yes
  • Relative Popularity 22680

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.
  • Main feature Expression profile and comparing datasets
  • Unique features

    Containing various data sets including different cancer types

  • Organism Human, Mouse, Rat
  • Category miRNA expression
  • Other covered categories
    Composite target prediction
    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. miRNA expression profiles can provide valuable clues for investigating the properties of miRNAs, such tissue specificity and differential expression in cancer/normal cell. Therefore, we performed the Q-PCR experiments for monitoring the expression profiles of 224 human miRNAs in eighteen major normal tissues in human .
  • Main feature Detecting miRNA expression in different organs
  • Unique features
    Expression profiles of 224 human miRNAs in 18 major normal tissues in human
  • Organism Human
  • Category miRNA expression
  • Other covered categories
    Composite target prediction
  • 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

miRNEYE

Additional Info

  • Activitiy Inactive
  • Description
    miRNeye presents survey of miRNA expression in ocular tissues, using both microarray and RNA in situ hybridization (ISH) procedures. We initially determined the expression profiles of miRNAs in the retina, lens, cornea and retinal pigment epithelium of the adult mouse eye by microarray. Each tissue exhibited notably distinct miRNA enrichment patterns and cluster analysis identified groups of miRNAs that showed predominant expression in specific ocular tissues or combinations of them.
  • Main feature miRNA expression profile of different parts of mouse eye
  • Unique features
    The expression patterns were generated by RNA in situ hybridization (ISH)
  • Organism Mouse
  • Category miRNA expression
  • Last observe Monday, 29 August 2016
  • Year published 2010
  • Citations per year 11.83
  • Last update Monday, 20 December 2010
  • Updated over past 3 years No
  • Relative Popularity 1134849

MirZ SmiRNAdb

Additional Info

  • Activitiy Inactive
  • Description
    Identifying miRNAs whose expression changes between cell types or between normal and pathological conditions is an important step towards characterizing their function as is the prediction of mRNAs that could be targeted by these miRNAs. MirZ developed to provide the community the possibility of exploring interactively miRNA expression patterns and the candidate targets of miRNAs in an integrated environment. The server provides experimental and computational biologists with statistical analysis and data mining tools operating on up-to-date databases of sequencing-based miRNA expression profiles in species ranging from Caenorhabditis elegans to Homo sapiens.
  • Main feature Expression profile of various tissues or cell lines
  • Unique features
    Comparison of different samples
    Comparison of different sets of samples
    Clustering of MiRNA Expression Profiles
  • Organism Human, Mouse, Other vertebrates, Insects, Nematodes
  • Category miRNA expression
  • Last observe Saturday, 27 August 2016
  • Year published 2009
  • Citations per year 7.85
  • Last update Thursday, 05 February 2009
  • Updated over past 3 years No
  • Relative Popularity 44261

SylArray

Additional Info

  • Activitiy Active
  • Description
    SylArray is a web-based resource designed for the analysis of large-scale expression datasets. It simply requires the user to submit a sorted list of genes from an expression experiment. SylArray utilizes curated sets of 3'UTRs to attach sequences to these genes and then applies the Sylamer algorithm for detection of miRNA or siRNA signatures in those sequences.
  • Main feature Automated identification of miRNA effects from expression data
  • Unique features
    Examine influence of small RNAs on expression profiles
  • Organism Human, Mouse, Other vertebrates, Insects, Nematodes, Rat
  • Category miRNA expression
  • Last observe Monday, 05 September 2016
  • Year published 2010
  • Citations per year 4.17
  • Last update Tuesday, 21 September 2010
  • Updated over past 3 years No
  • Relative Popularity 27182

YM500v2

Additional Info

  • Activitiy Active
  • Description
    YM500 is an integrated database for miRNA quantification, isomiR identification, arm switching discovery and novel miRNA prediction from small RNA sequencing (smRNA-seq). In this update of YM500, we focus on the cancer miRNAome to make the database more disease-orientated. There are more than 8,000 cancer-related smRNA-seq datasets (including those of primary tumours, paired normal tissues, PBMC, and metastatic tissues) incorporated into YM500v2.
  • Main feature Detecting miRNA expression in various organs
  • Unique features
    Isomir identification Arm switching discovery and novel miRNA prediction from small RNA sequencing
  • Organism Human
  • Category miRNA expression
  • Other covered categories
    miRNA roles in diseases
  • Last observe Friday, 02 September 2016
  • Year published 2013
  • Citations per year 7.33
  • Last update Wednesday, 29 October 2014
  • Updated over past 3 years Yes
  • Relative Popularity 89820

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 Differential Expression Analysis
  • Unique features
    Select and compare groups of microRNA or mRNA expression samples from the extensive DIANA expression database
  • Organism Human, Mouse
  • Category miRNA expression
  • Other covered categories
    miRNA gene regulation
  • Last observe Wednesday, 31 August 2016
  • Year published 2010
  • Citations per year 9
  • Last update Friday, 20 May 2016
  • Updated over past 3 years Yes
  • Relative Popularity 2310477

ExcellmiRDB

Additional Info

  • Activitiy Active
  • Description
    ExcellmiRDB provides integrated information about miRNAs levels in biofluids in a user-friendly way. ExcellmiRDB is the only one specialized for storing curated data on miRNA levels in biofluid samples. At present, ExcellmiRDB has 2773 disease-extracellular miRNAs and 1108 biofluid-extracellular miRNAs relationships curated from 108 articles selected from more than 600 surveyed PubMed abstracts.
  • Main feature Extracellular miRNAs
  • Unique features
    miRNA-disease associations along with expression pattern and number of articles Network visualize miRNA body fluid associations
  • Organism Human, Mouse, Other vertebrates, Rat
  • Category miRNA expression
  • Last observe Monday, 29 August 2016
  • Year published 2015
  • Citations per year 3
  • Last update Tuesday, 06 January 2015
  • Updated over past 3 years Yes
  • Relative Popularity 0

mESAdb

Additional Info

  • Activitiy Active
  • Description
    mESAdb is a regularly updated database for the multivariate analysis of sequences and expression of microRNAs from multiple taxa. The database primarily comprises mature microRNA sequences and their target data, along with selected human, mouse and zebrafish expression data sets. mESAdb analysis modules allow (i) mining of microRNA expression data sets for subsets of microRNAs selected manually or by motif; (ii) pair-wise multivariate analysis of expression data sets within and between taxa; and (iii) association of microRNA subsets with annotation databases, HUGE Navigator, KEGG and GO.
  • Main feature Expression profiles of various datasets
  • Unique features
    Mining of microRNA expression data sets for subsets of microRNAs
    Comparison different miRNA expression datasets
    Association of microRNA subsets with annotation databases, HUGE Navigator, KEGG and GO
  • Organism Human, Mouse, Other vertebrates
  • Category miRNA expression
  • Last observe Friday, 26 August 2016
  • Year published 2011
  • Citations per year 2.8
  • Last update Saturday, 01 January 2011
  • Updated over past 3 years Yes
  • Relative Popularity 47214

miRandola

Additional Info

  • Activitiy Active
  • Description
    miRandola is a manually curated database of circulating miRNAs. The database catalogs information from both published (from literature and public resources) and unpublished studies (from direct researchers submission). The database include information about miRNAs and their extracellular form, samples, fluids and data sources.
  • Main feature Circulating non-coding RNAs
  • Unique features
    Extracellular/Circulating non-coding RNAs
  • Organism Human
  • Category miRNA expression
  • Last observe Monday, 29 August 2016
  • Year published 2012
  • Citations per year 16
  • Last update Friday, 19 October 2012
  • Updated over past 3 years Yes
  • Relative Popularity 26282

mirEX 2.0

Additional Info

  • Activitiy Active
  • Description
    The mirEX 2.0 provides a comprehensive platform for the exploration of microRNA expression data based on quantitative Real Time PCR and NGS sequencing experiments, covering various developmental stages, from wild-type to mutant plants. The portal includes mature and pri-miRNA expression levels detected in three plant species (Arabidopsis thaliana, Hordeum vulgare and Pellia endiviifolia), and in A. thaliana miRNA biogenesis pathway mutants.
  • Main feature Expression profiling of plant microRNAs.
  • Unique features
    MicroRNAs from wild-type and mutant plants
    Based on quantitative Real Time PCR and sequencing experiments
  • Organism Plants
  • Category miRNA expression
  • Last observe Wednesday, 31 August 2016
  • Year published 2015
  • Citations per year 2
  • Last update Tuesday, 16 June 2015
  • Updated over past 3 years Yes
  • Relative Popularity 0

miRStress

Additional Info

  • Activitiy Inactive
  • Description
    miRStress database describes the changes in miRNA levels following an array of stress types in eukaryotic cells. To validate the database we performed a cross-species analysis to identify miRNAs that respond to radiation. The miRStress tool, which can be used to uncover new insight into the biological roles of miRNAs, and also has the potential to unearth potential biomarkers for therapeutic response.
  • Main feature Stress and miRNA association
  • Unique features
    MicroRNA deregulation following exposure to different stress stimuli
  • Organism Human, Mouse, Other vertebrates, Rat
  • Category miRNA expression
  • Last observe Wednesday, 31 August 2016
  • Year published 2013
  • Citations per year 2.33
  • Last update Tuesday, 05 August 2014
  • Updated over past 3 years Yes
  • Relative Popularity 49414

PmiRExAt

Additional Info

  • Activitiy Active
  • Description
    MirZ developed to provide the community the possibility of exploring interactively miRNA expression patterns and the candidate targets of miRNAs in an integrated environment. The server provides statistical analysis and data mining tools operating on up-to-date databases of sequencing-based miRNA expression profiles.
  • Main feature Expression profiling of plant microRNAs.
  • Unique features
    The most comprehensive comparative view of plant miRNA expression
    In multiple tissues and developmental stages
  • Organism Plants
  • Category miRNA expression
  • Last observe Friday, 26 August 2016
  • Year published 2016
  • Citations per year 0
  • Last update Wednesday, 23 March 2016
  • Updated over past 3 years Yes
  • Relative Popularity 993311

PMTED

Additional Info

  • Activitiy Inactive
  • Description
    Plant MiRNA Target Expression Database (PMTED) is designed to retrieve and analyze expression profiles of miRNA targets represented in the plethora of existing microarray data that are manually curated. It provides a Basic Information query function for miRNAs and their target sequences, gene ontology, and differential expression profiles. It also provides searching and browsing functions for a global Meta-network among species, bioprocesses, conditions, and miRNAs, meta-terms curated from well annotated microarray experiments. Networks are displayed through a Cytoscape Web-based graphical interface. PMTED provides a target prediction portal for user-defined novel miRNAs and corresponding target expression profile retrieval.
  • Main feature Expression profiles of miRNA targets
  • Unique features
    Provides information on query function of plant miRNAs and their target sequences, gene ontology, and differential expression profiles
  • Organism Plants
  • Category miRNA expression
  • Last observe Monday, 29 August 2016
  • Year published 2013
  • Citations per year 3.67
  • Last update Saturday, 26 May 2012
  • Updated over past 3 years Yes
  • Relative Popularity 0

SM2miR

Additional Info

  • Activitiy Active
  • Description
    SM2miR provides a fairly comprehensive repository about the influences of small molecules on miRNA expression, which will promote the development of miRNA therapeutics. SM2miR database recorded 2925 relationships between 151 small molecules and 747 miRNAs in 17 species after manual curation from nearly 2000 articles. Each entry contains the detailed information about small molecules, miRNAs and evidences of their relationships, such as species, miRBase Accession number, DrugBank Accession number, PubChem Compound Identifier (CID), expression pattern of miRNA, experimental method, tissues or conditions for detection.
  • Main feature Expression of miRNAs
  • Unique features
    Experimentally validated small molecules' effects on microRNA expression
    Search by miRNA or small molecule
  • Organism Human
  • Category miRNA expression
  • Last observe Wednesday, 31 August 2016
  • Year published 2013
  • Citations per year 4
  • Last update Monday, 27 April 2015
  • Updated over past 3 years Yes
  • Relative Popularity 0

SurvMicro

Additional Info

  • Activitiy Active
  • Description
    SurvMicro assesses miRNA signatures from publicly available miRNA profiles using multivariate survival analysis. SurvMicro is composed of a wide and updated database of >40 cohorts in different tissues and a web tool where survival analysis can be done in minutes. We presented evaluations to portray the straightforward functionality of SurvMicro in liver and lung cancer.
  • Main feature Expression of miRNAs
  • Unique features
    Assesses miRNA signatures from publicly available miRNA profiles
  • Organism Human
  • Category miRNA expression
  • Last observe Friday, 02 September 2016
  • Year published 2014
  • Citations per year 2.5
  • Last update Friday, 09 September 2016
  • Updated over past 3 years Yes
  • Relative Popularity 6916