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1 Antagomirbase A database based on putative antagomirs-miRNA heterodimers. In this work, the human miRNA dataset was used as template to design putative antagomirs, using GC content and secondary structures as parameters. The algorithm used predicted the free energy of unbound antagomirs.
  • human
  • miRNA-ncRNA interaction
  • Homepage

    Publication
    Aug. 20, 2011
    Citations: 1
    2 CircuitsDB2 CircuitsDB 2 contains a large number of regulatory circuits, composed by Transcription Factors, target genes, microRNAs and lincRNAs interacting together, in the human genome. The resulting integrated network can be the starting point for a deeper understanding of their system-level properties and provides candidates for experimental validation.
  • human
  • predicted target
  • miRNA-ncRNA interaction
  • transcription factor-miRNA regulation
  • Homepage

    Publication
    Aug. 23, 2010
    Citations: 41
    3 CoGemiR CoGeMiR is a publicily available microRNA-centered database whose aim is to offer an overview of the conservation of microRNAs during evolution in different animal species. This database collects information on genomic location, conservation and expression data of both known and predicted microRNAs.
  • worm
  • fish
  • fly
  • chicken
  • human
  • mouse
  • rat
  • other animals (selectable)
  • miRNA basic information
  • miRNA expression
  • Homepage

    Publication
    Oct. 6, 2008
    Citations: 11
    4 CREAM CREAM (Chemotherapy ResistancE-Associated MiRSNP Database) is a free online database depositing the functional miRSNP associated with chemotherapy resistance.
  • human
  • miRNA basic information
  • predicted target
  • diseases/pathways
  • miRNA-SNP related informations
  • Homepage

    Publication
    May 29, 2014
    Citations: 1
    5 dbDEMC 2.0 dbDEMC (database of Differentially Expressed MiRNAs in human Cancers) is an integrated database that designed to store and display differentially expressed microRNAs (miRNAs) in human cancers detected by high-throughput methods. In this updated version of dbDEMC, a total of 209 expression profiling data sets across 36 cancer types and 73 subtypes, and a total of 2224 differentially expressed miRNAs were identified.
  • human
  • diseases/pathways
  • miRNA expression
  • Homepage

    Publication
    Jan. 4, 2017
    Citations: 9
    6 DIANA-LncBase v2 DIANA-LncBase is first extensive database dedicated to cataloging miRNA:lncRNA interactions, providing the largest collection of experimentally supported and in silico predicted MREs on lncRNAs.
  • human
  • mouse
  • diseases/pathways
  • miRNA-ncRNA interaction
  • Homepage

    Publication
    Nov. 26, 2015
    Citations: 29
    7 DIANA-TarBase Provides for the first time hundreds of thousands of high quality manually curated experimentally validated miRNA:gene interactions, enhanced with detailed meta-data. With DIANA-TarBase v7.0 you can easily identify positive or negative experimental results, the utilized experimental methodology, experimental conditions including cell/tissue type and treatment. The new interface provides also advanced information ranging from the binding site location, as identified experimentally as well as in silico, to the primer sequences used for cloning experiments
  • animals
  • plants
  • viruses
  • miRNA basic information
  • target experimental
  • predicted target
  • diseases/pathways
  • target expression
  • Homepage

    Publication
    Nov. 21, 2014
    Citations: 186
    8 DMD The Dietary microRNA Database is a searchable database of published and novel microRNA sequences discovered in human food. The annotation covers the hairpin structure of the pre-microRNAs, cross-species sequence comparison on each mature microRNA, reported disease relevance, and the experimentally validated gene targets, of which a gene regulation network was built for each entry. DMD can be also used to generate a list of features for use in machine learning applications. It is split up into two major categories: Primary, and Secondary. The Primary features are all sequence based features while the Secondary features are based on structural attributes.
  • human
  • chicken
  • fish
  • animals
  • plants
  • miRNA basic information
  • target experimental
  • predicted target
  • diseases/pathways
  • Homepage

    Publication
    June 1, 2015
    Citations: 9
    9 EpimiR EpimiR comprehensive database which store the experimentally validated mutual regulations between epigenetic modifications and miRNAs.
  • human
  • mouse
  • rat
  • chicken
  • Epstein Barr Virus
  • Arabidopsis thaliana
  • miRNA basic information
  • target experimental
  • miRNA expression
  • Homepage

    Publication
    March 28, 2014
    Citations: 7
    10 EpimiRBase EpimiRBase is a manually curated databasefor researchers interested in the role of microRNAs in epilepsy. The fully-searchable database includes information on up- and downregulated microRNAs in the brain and blood, as well as functional studies, and covers both rodent models and human epilepsy.
  • human
  • mouse
  • rat
  • diseases/pathways
  • literature mining
  • miRNA expression
  • Homepage

    Publication
    Jan. 8, 2016
    Citations: 6
    11 ExcellmiRDB A curated online database that provides integrated information about miRNAs levels in biofluids in a user-friendly way. Although many miRNA databases, including disease-oriented databases, have been launched before, the ExcellmiRDB is so far the only one specialized for storing curated data on miRNA levels in biofluid samples.
  • vertebrates
  • diseases/pathways
  • miRNA expression
  • Homepage

    Publication
    Jan. 6, 2015
    Citations: 1
    12 HMDD A repository of miRNA-associated diseases, obtained by manual curation from literature data. HMDD v2.0 presents more detailed and comprehensive annotations to the human miRNA-disease association data, including miRNA-disease association data from the evidence of genetics, epigenetics, circulating miRNAs, and miRNA-target interactions.
  • human
  • target experimental
  • diseases/pathways
  • literature mining
  • Homepage

    Publication
    Nov. 4, 2013
    Citations: 137
    13 HOCTARdb The HOCTAR database (db) is a publicly available resource collecting ranked list of predicted target genes for 290 intragenic miRNAs annotated in human. HOCTARdb is a unique resource that integrates miRNA target prediction genes and transcriptomic data to score putative miRNA targets looking at the expression behavior of their host genes.
  • human
  • predicted target
  • diseases/pathways
  • Homepage

    Publication
    March 22, 2011
    Citations: 20
    14 mESAdb A regularly updated database for the multivariate analysis of sequences and expression of microRNAs from multiple taxa. mESAdb is modular and has a user interface implemented in PHP and JavaScript and coupled with statistical analysis and visualization packages written for the R language.
  • human
  • mouse
  • fish
  • miRNA basic information
  • predicted target
  • diseases/pathways
  • miRNA expression
  • Homepage

    Publication
    Dec. 22, 2010
    Citations: 10
    15 MicroCosm Targets A web resource developed by the Enright Lab at the EMBL-EBI containing computationally predicted targets for microRNAs across many species.
  • animals
  • predicted target
  • Homepage

    Publication
    Dec. 23, 2007
    Citations: 1680
    16 microPIR2 MicroPIR2 is public database containing over 80 and 40 million predicted microRNA target sites located within human and mouse promoter sequences. These predicted targets are presented along with their related genomic and experimental data.
  • human
  • mouse
  • miRNA basic information
  • target experimental
  • predicted target
  • diseases/pathways
  • miRNA expression
  • transcription factor-miRNA regulation
  • miRNA-SNP related informations
  • Homepage

    Publication
    Nov. 25, 2014
    Citations: 3
    17 microRNA.org A comprehensive resource of microRNA target predictions and expression profiles. Target predictions are based on a development of the miRanda algorithm which incorporates current biological knowledge on target rules and on the use of an up-to-date compendium of mammalian microRNAs. 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.
  • human
  • mouse
  • rat
  • worm
  • fly
  • miRNA basic information
  • predicted target
  • miRNA expression
  • Homepage

    Publication
    Dec. 23, 2007
    Citations: 867
    18 microRNAviewer / miRviewer miRviewer provides a comprehensive view of all known miRNAs in annotated animal genomes. microRNAviewer exhibits a comprehensive set of miRNA genes both from miRBase and candidate homologs identified using miRNAminer. Additional layers of information, such as conservation, multiple alignments of the sequences, indication of mutated miRNAs, genomic loci and secondary structure, are also available.
  • animals
  • miRNA basic information
  • Homepage

    Publication
    Feb. 13, 2012
    Citations: 20
    19 mimiRNA A database of miRNA expression profile data across different tissues and cell lines. mimiRNA incorporates a sample classification algorithm, ExParser, that groups identical miRNA or mRNA experiments from separate sources. This enables mimiRNA to provide reliable expression profiles and to discover functional relations between miRNAs and mRNAs such as miRNA targets.
  • human
  • miRNA basic information
  • predicted target
  • diseases/pathways
  • target expression
  • miRNA expression
  • Homepage

    Publication
    Nov. 17, 2009
    Citations: 31
    20 miR2Disease miR2Disease, a manually curated database, aims at providing a comprehensive resource of miRNA deregulation in various human diseases. Each entry contains detailed information on a miRNA-disease relationship, including miRNA ID, disease name, a brief description of the miRNA-disease relationship, miRNA expression pattern in the disease state, detection method for miRNA expression, experimentally verified miRNA target gene(s), and literature reference.
  • human
  • miRNA basic information
  • target experimental
  • predicted target
  • diseases/pathways
  • literature mining
  • miRNA expression
  • Homepage

    Publication
    Jan. 1, 2009
    Citations: 377
    21 miRandola A comprehensive classification of different extracellular circulating miRNA types. A direct link to the knowledge base miRò together with the inclusion of datamining facilities allow users to infer possible biological functions of the circulating miRNAs and their connection with the phenotype.
  • human
  • miRNA basic information
  • diseases/pathways
  • miRNA expression
  • Homepage

    Publication
    Oct. 19, 2012
    Citations: 59
    22 miRBase The miRBase database is a searchable database of published miRNA sequences and annotation. Each entry represents a predicted hairpin portion of a miRNA transcript (termed mir in the database), with information on the location and sequence of the mature miRNA sequence (termed miR). Both hairpin and mature sequences are available for searching and browsing, and entries can also be retrieved by name, keyword, references and annotation.
  • animals
  • plants
  • viruses
  • miRNA basic information
  • target experimental
  • predicted target
  • miRNA expression
  • Homepage

    Publication
    Nov. 25, 2013
    Citations: 1335
    23 miRBase Tracker miRBase Tracker is a framework on top of miRBase that, in addition to providing miRBase's basic annotation information, allows researchers to keep track of miRNA annotation changes and facilitates reannotation.
  • any (from miRBase)
  • miRNA basic information
  • Homepage

    Publication
    Aug. 24, 2014
    Citations: 30
    24 miRCancer miRCancer provides comprehensive collection of microRNA (miRNA) expression profiles in various human cancers which are automatically extracted from published literatures in PubMed. It utilizes text mining techniques for information collection. Manual revision is applied after auto-extraction to provide 100% precision.
  • human
  • diseases/pathways
  • literature mining
  • miRNA expression
  • Homepage

    Publication
    Jan. 16, 2013
    Citations: 74
    25 miRDB Recently updated features of miRDB, includes 2.1 million predicted gene targets regulated by 6709 miRNAs. In addition to presenting precompiled prediction data, a new feature is the web server interface that allows submission of user-provided sequences for miRNA target prediction. In this way, users have the flexibility to study any custom miRNAs or target genes of interest.
  • human
  • mouse
  • rat
  • dog
  • chicken
  • miRNA basic information
  • predicted target
  • literature mining
  • Homepage

    Publication
    Nov. 5, 2014
    Citations: 231
    26 miRdSNP A database of manually curated dSNPs on the 3'UTRs of human genes from available publications in PubMed. The advanced web interface allows users to perform proximity searches between miRNA target sites and dSNPs by gene name, miRbase ID, target prediction algorithm, disease, and any nucleotide distance between dSNPs and miRNA target sites.
  • human
  • target experimental
  • predicted target
  • diseases/pathways
  • miRNA-SNP related informations
  • Homepage

    Publication
    Jan. 25, 2012
    Citations: 54
    27 miRecords A resource for animal miRNA-target interactions. miRecords consists of two components. The Validated Targets component is a large, high-quality database of experimentally validated miRNA targets resulting from meticulous literature curation. The Predicted Targets component of miRecords is an integration of predicted miRNA targets produced by 11 established miRNA target prediction programs.
  • human
  • mouse
  • rat
  • fly
  • worm chicken
  • fish
  • other animals (selectable)
  • miRNA basic information
  • target experimental
  • predicted target
  • target expression
  • Homepage

    Publication
    Jan. 1, 2009
    Citations: 482
    28 miREnvironment miREnvironment is a database that curated and collected experimentally supported microRNA (miRNA), one class of newly identified genetic factors, and environmental factor interplays and their associated phenotypes. It also has a tool performing bioinformatic analysis to predict the result of cancer treatment and associations between EFs and human disease.
  • animals
  • plants
  • viruses
  • miRNA basic information
  • diseases/pathways
  • miRNA expression
  • Homepage

    Publication
    Oct. 7, 2011
    Citations: 23
    29 mirEX 2.0 mirEX2 is a comprehensive platform for comparative analysis of primary microRNA expression data. RT–qPCR-based gene expression profiles are stored in a universal and expandable database scheme and wrapped by an intuitive user-friendly interface.
  • plants
  • miRNA basic information
  • miRNA expression
  • Homepage

    Publication
    June 16, 2015
    Citations: 10
    30 miRGate 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.
  • human
  • mouse
  • rat
  • target experimental
  • predicted target
  • Homepage

    Publication
    April 8, 2015
    Citations: 15
    31 miRGator Aims to be the microRNA (miRNA) portal encompassing microRNA diversity, expression profiles, target relationships, and various supporting tools. By keeping datasets and analytic tools up-to-date, miRGator should continue to serve as an integrated resource for biogenesis and functional investigation of miRNAs.
  • human
  • miRNA basic information
  • target experimental
  • predicted target
  • diseases/pathways
  • target expression
  • miRNA expression
  • Homepage

    Publication
    Nov. 27, 2012
    Citations: 36
    32 DIANA-miRGen v3.0 Aim of DIANA-miRGen v3.0 is to provide for the first time 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. The database currently supports 276 miRNA TSSs that correspond to 428 precursors and >19M binding sites of 202 TFs on a genome-wide scale in nine cell-lines and six tissues of Homo sapiens and Mus musculus.
  • human
  • mouse
  • diseases/pathways
  • target expression
  • transcription factor-miRNA regulation
  • Homepage

    Publication
    Nov. 19, 2015
    Citations: 13
    33 MirGeneDB.org MirGeneDB.org is the curated microRNA gene database that We established MirGeneDB —to catalog this set of miRNAs, which complements the efforts of miRBase but differs from it by annotating the mature versus star products and by imposing an evolutionary hierarchy upon this curated and consistently named repertoire. Currently entries for human, mouse, zebra fish and chicken are available. Expansion is planned for summer 2017
  • mouse
  • human
  • chicken
  • fish
  • miRNA basic information
  • target experimental
  • predicted target
  • miRNA expression
  • Homepage

    Publication
    Sept. 1, 2015
    Citations: 66
    34 miRNA SniPer An online tool for the detection of miRNA polymorphisms in vertebrates. miRNA SNiPer accepts a list of miRNA genes and returns a table of variations within different regions of miRNA genes: pre-miRNA, mature, seed region.
  • human
  • mouse
  • chicken
  • rat
  • fish
  • fly
  • other animals (selectable)
  • plants (selectable)
  • miRNA basic information
  • miRNA-SNP related informations
  • Homepage

    Publication
    Jan. 27, 2012
    Citations: 24
    35 miRNA - Target Gene Prediction at EMBL This database provides access to the 2003 and 2005 miRNA-Target predictions for Drosophila miRNAs.
  • fly
  • target experimental
  • predicted target
  • Homepage

    Publication
    Feb. 15, 2005
    Citations: 756
    36 miRNAMap miRNAMap 2.0 collects experimentally verified microRNAs and experimentally verified miRNA target genes in human, mouse, rat and other metazoan genomes. Three computational tools, miRanda, RNAhybrid and TargetScan, were employed to identify miRNA targets in 3'-UTR of genes as well as the known miRNA targets. Additionally, miRNA expression profiles can provide valuable clues on the characteristics of miRNAs, including tissue specificity and differential expression in cancer/normal cell.
  • human
  • mouse
  • fly
  • worm
  • fish
  • rat
  • chicken
  • other animals (selectable)
  • miRNA basic information
  • target experimental
  • predicted target
  • target expression
  • miRNA expression
  • Homepage

    Publication
    Dec. 23, 2007
    Citations: 105
    37 miRNEST A integrative collection of animal, plant and virus microRNA data. In its updated version miRNEST 2.0, the database is complemented with our extensive miRNA predictions from deep sequencing libraries, data from plant degradome analyses, results of pre-miRNA classification with HuntMi and miRNA splice sites information.
  • plants
  • animals
  • viruses
  • miRNA basic information
  • target experimental
  • predicted target
  • miRNA expression
  • Homepage

    Publication
    Nov. 15, 2013
    Citations: 8
    38 miROrtho miROrtho contains predictions of precursor miRNA genes covering several animal genomes combining orthology and a Support Vector Machine. We provide homology extended alignments of already known miRBase families and putative miRNA families exclusively predicted by our SVM and orthology pipeline.
  • animals
  • miRNA basic information
  • Homepage

    Publication
    Jan. 1, 2009
    Citations: 32
    39 miRPathDB miRPathDB aim to augment available target pathway web-servers by providing researches easy access to the information which pathways are regulated by a miRNA, which miRNAs target a pathway and how specific the regulations are. The database contains a large number of miRNAs, different miRNA target sets and a broad selection of functional biochemical categories. In addition to H. sapiens, also M. musculus data are stored and can be compared to human target pathways.
  • human
  • mouse
  • target experimental
  • predicted target
  • diseases/pathways
  • Homepage

    Publication
    Oct. 13, 2016
    Citations: 10
    40 mirPub mirPub is a database and a related web application which provides a powerful and intuitive interface to the researchers that want to search for publications related to particular microRNA molecules. mirPub also provides useful information about the correlation of these microRNAs to any diseases, tissues and genes. It facilitates publication search by considering microRNA families and the history of the microRNA nomenclature.
  • any
  • miRNA basic information
  • literature mining
  • Homepage

    Publication
    Dec. 20, 2014
    Citations: 6
    41 miRSel Automated extraction of associations between microRNAs and genes from the biomedical literature. miRSel is updated daily and can be queried using a web-based interface via microRNA identifiers, gene and protein names, PubMed queries as well as gene ontology (GO) terms.
  • human
  • mouse
  • rat
  • miRNA basic information
  • target experimental
  • predicted target
  • diseases/pathways
  • literature mining
  • Homepage

    Publication
    March 16, 2010
    Citations: 29
    42 MirSNP MirSNP is a collection of human SNPs in predicted miRNA-mRNA binding sites.
  • human
  • miRNA basic information
  • predicted target
  • miRNA-SNP related informations
  • Homepage

    Publication
    Nov. 23, 2012
    Citations: 69
    43 miRStress The miRStress database is a comprehensive resource that documents microRNA deregulation following exposure to different stress stimuli.
  • human
  • mouse
  • rat
  • fish
  • pig
  • miRNA basic information
  • literature mining
  • miRNA expression
  • Homepage

    Publication
    Nov. 14, 2013
    Citations: 7
    44 miRSystem A database which integrates seven well known miRNA target gene prediction programs: DIANA, miRanda, miRBridge, PicTar, PITA, rna22, and TargetScan. This database contains validated data from TarBase and miRecords on interaction between miRNA and its target genes.
  • human
  • mouse
  • miRNA basic information
  • target experimental
  • predicted target
  • diseases/pathways
  • Homepage

    Publication
    Aug. 1, 2012
    Citations: 75
    45 miRTarBase miRTarBase provides information about experimentally validated miRNA-target interactions (MTIs). The latest update of the miRTarBase expanded it to identify systematically Argonaute-miRNA-RNA interactions from 138 crosslinking and immunoprecipitation sequencing (CLIP-seq) data sets that were generated by 21 independent studies. The database contains 4966 articles, 7439 strongly validated MTIs (using reporter assays or western blots) and 348 007 MTIs from CLIP-seq. The number of MTIs in the miRTarBase has increased around 7-fold since the 2014 miRTarBase update.
  • animals
  • plants
  • viruses
  • miRNA basic information
  • target experimental
  • predicted target
  • diseases/pathways
  • literature mining
  • target expression
  • miRNA expression
  • Homepage

    Publication
    Nov. 20, 2015
    Citations: 291
    46 miRWalk A publicly available comprehensive resource, hosting the predicted as well as the experimentally validated microRNA (miRNA)-target interaction pairs.
  • human
  • mouse
  • rat
  • miRNA basic information
  • target experimental
  • predicted target
  • diseases/pathways
  • literature mining
  • miRNA-ncRNA interaction
  • target expression
  • miRNA expression
  • Homepage

    Publication
    July 30, 2015
    Citations: 207
    47 MtiBase MtiBase (MiRNA-target interactions database) is a database that identify CDS-located and 5'UTR-located miRNA binding sites and systematically evaluate miRNA regulatory effects on mRNA stability and translation by integrating multiple high-throughput experimental datasets such as Ago CLIP-Seq (HITS-CLIP, PAR-CLIP, iCLIP, CLASH), mRNA profiles, ribisome-protected fragment sequencing (RPF) and pulsed stable isotope labeling with amino acids in culture (pSILAC). The SNP influence to the regulatory effects of CDS-located and 5'UTR-located miRNA binding sites was also systematically investigated.
  • human
  • mouse
  • target experimental
  • predicted target
  • target expression
  • miRNA expression
  • miRNA-SNP related informations
  • Homepage

    Publication
    Oct. 1, 2015
    Citations: 9
    48 multiMiR A miRNA-target interaction R package and database, which includes: (i) compilation of nearly 50 million records in human and mouse from 14 different databases, more than any other collection; (ii) expansion of databases to those based on disease annotation and drug microRNA response, in addition to many experimental and computational databases; and (iii) user-defined cutoffs for predicted binding strength to provide the most confident selection.
  • human
  • mouse
  • target experimental
  • predicted target
  • diseases/pathways
  • Homepage

    Publication
    July 24, 2014
    Citations: 38
    49 OncomiRDB oncomiRDB database aimes at annotating the experimentally verified oncogenic and tumor-suppressive miRNAs from literature. This database only collects items having direct functional evidences: 1) the miRNA regulates at least one cancer-related phenotype or cellular process (such as proliferation, apoptosis, migration and invasion, senescence and cell cycle regulation); or 2) the miRNA directly regulates at least one oncogenic or tumor-suppressive gene verified by luciferase reporter assay.
  • human
  • target experimental
  • diseases/pathways
  • literature mining
  • miRNA expression
  • Homepage

    Publication
    March 20, 2014
    Citations: 28
    50 OncomiRdbB OncomiRdbB is an integrated database consisting of the miRNAs of human and mouse genomes, their sequences, chromosome and gene locations, respective targets and their description, pathways it regulates in breast cancer.The miRNAs were mined from miRBase, Phenomir, Mir2Disease etc and their respective sequences were obtained from miRbase. Their target genes were computationally derived from different oncogenic pathways such as wnt, Jak- Stat, MAPK, mTOR, VEGF, Apoptosis and Notch pathways and their genomic sequences from ENSEMBLE- BioMart. Additionally, we have also listed the experimentally validated novel microRNAs for human breast cancer.
  • human
  • mouse
  • target experimental
  • predicted target
  • diseases/pathways
  • literature mining
  • Homepage

    Publication
    Jan. 15, 2014
    Citations: 3
    51 PASmiR PASmiR, a literature-curated and web-accessible database, was developed to provide a solid platform for collection, standardization, and searching of these miRNA-stress regulation data in plants. As such this database will be a comprehensive repository for miRNA regulatory mechanisms involved in plant response to abiotic stresses in the plant stress physiology community.
  • plants
  • miRNA basic information
  • target experimental
  • miRNA expression
  • Homepage

    Publication
    March 1, 2013
    Citations: 15
    52 PhenomiR The PhenomiR database provides information about differentially regulated miRNA expression in diseases and other biological processes. The content of PhenomiR is completely generated by manual curation of experienced annotators. The design principle of PhenomiR is to use established ontologies and resources.
  • human
  • target experimental
  • diseases/pathways
  • target expression
  • miRNA expression
  • Homepage

    Publication
    Jan. 20, 2010
    Citations: 68
    53 PmiRExAt PmiRExAt is a new online web resource that provides the most comprehensive comparative view yet of plant microRNAs (miRNAs) expression in multiple tissues, developmental stages of wheat, rice and maize. Meta-analysis of the publicly available small RNA datasets showed significant expression patterns of several miRNAs. This web resource and service can be used by plant science community to study expression patterns of miRNAs. PmiRExAt application program interface, a simple object access protocol web service allows other programmers to remotely invoke the methods written for doing programmatic search operations on PmiRExAt database.
  • plants
  • predicted target
  • literature mining
  • miRNA expression
  • Homepage

    Publication
    April 13, 2016
    Citations: 2
    54 PMTED 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 plant miRNAs and their target sequences, gene ontology, and differential expression profiles.
  • plants
  • target experimental
  • diseases/pathways
  • target expression
  • Homepage

    Publication
    June 3, 2013
    Citations: 10
    55 PNRD It is the updated version of PMRD. PNRD mainly focuses on plant species. A total of 25739 entries of 11 different types of ncRNAs from 150 plant species were collected. Targets of miRNAs were extended to 178138 pairs in 46 species, while the number of miRNA expression profiles reached 35. Improvements in PNRD are not only the larger amounts of data, but also better service, such as a more user-friendly interface, more multifunctional and browsing options and more background data for users to download.
  • plants
  • miRNA basic information
  • target experimental
  • predicted target
  • literature mining
  • miRNA-ncRNA interaction
  • miRNA expression
  • Homepage

    Publication
    Nov. 14, 2014
    Citations: 29
    56 PolymiRTS Database An integrated platform for analyzing the functional impact of genetic polymorphisms in miRNA seed regions and miRNA target sites. The browse and search pages of PolymiRTS allow users to explore the relations between the PolymiRTSs and gene expression traits, physiological and behavioral phenotypes, human diseases and biological pathways.
  • human
  • mouse
  • miRNA basic information
  • target experimental
  • predicted target
  • diseases/pathways
  • miRNA-SNP related informations
  • Homepage

    Publication
    Oct. 24, 2013
    Citations: 72
    57 PuTmiR Focus on TF to miRNA regulation and provide a novel interface for extracting the list of putative TFs for human miRNAs.
  • human
  • transcription factor-miRNA regulation
  • Homepage

    Publication
    April 15, 2010
    Citations: 15
    58 SomamiR DB 2.0 SomamiR is a database of cancer somatic mutations in microRNAs (miRNA) and their target sites that potentially alter the interactions between miRNAs and competing endogenous RNAs (ceRNA) including mRNAs, circular RNAs (circRNA) and long noncoding RNAs (lncRNA). It also provides an integrated platform for the functional analysis of these somatic mutations. Additionally, the SomamiR DB contains a collection of somatic and germline mutations in miRNAs or their target sites that have been strongly linked with cancer. Specifically, the majority of these mutations met the following criteria (a) they have been associated with cancer risk in GWAS or CGAS and (b) there is experimental evidence indicating that the mutation alters miRNA function
  • human
  • target experimental
  • predicted target
  • diseases/pathways
  • miRNA-ncRNA interaction
  • miRNA-SNP related informations
  • Homepage

    Publication
    Nov. 17, 2015
    Citations: 14
    59 starBase It is designed for decoding Pan-Cancer and Interaction Networks of lncRNAs, miRNAs, competing endogenous RNAs(ceRNAs), RNA-binding proteins (RBPs) and mRNAs from large-scale CLIP-Seq data and tumor samples. starBase is also developed for deciphering Protein-RNA and miRNA-target interactions, such as protein-lncRNA, protein-sncRNA, protein-mRNA, protein-pseudogene, miRNA-lncRNA, miRNA-mRNA, miRNA-circRNA, miRNA-pseudogene, miRNA-sncRNA interactions and ceRNA networks from CLIP-Seq datasets.
  • human
  • mouse
  • worm
  • target experimental
  • predicted target
  • diseases/pathways
  • miRNA-ncRNA interaction
  • target expression
  • miRNA expression
  • transcription factor-miRNA regulation
  • Homepage

    Publication
    Dec. 1, 2013
    Citations: 393
    60 targetHub A CouchDB database of miRNA-gene interactions. TargetHub provides a programmer-friendly interface to access miRNA targets. The Web site provides RESTful access to miRNA-gene interactions with an assortment of gene and miRNA identifiers. It can be a useful tool to integrate miRNA target interaction data directly into high-throughput bioinformatics analyses.
  • human
  • miRNA basic information
  • target experimental
  • predicted target
  • Homepage

    Publication
    Sept. 6, 2013
    Citations: 5
    61 TargetScanS Database of microRNA targets conserved in 5 vertebrates.
  • vertebrates
  • predicted target
  • Homepage

    Publication
    Jan. 14, 2005
    Citations: 4158
    62 TMREC TMREC provides the detailed cascade regulations of TF-miRNA in the context of human diseases, which enable the experimental biologist to understand the transcriptional and post-transcriptional regulatory mechanisms in specific disease, and identify the potential therapeutic targets in the upstream of the cascades.
  • human
  • target experimental
  • diseases/pathways
  • transcription factor-miRNA regulation
  • Homepage

    Publication
    May 1, 2015
    Citations: 4
    63 TransmiR A database for transcription factor-microRNA regulations.
  • animals
  • plants
  • diseases/pathways
  • literature mining
  • transcription factor-miRNA regulation
  • Homepage

    Publication
    Sept. 28, 2009
    Citations: 142
    64 Vir-Mir db Vir-Mir database, a database containing predicted viral miRNA candidate hairpins.
  • viruses
  • miRNA basic information
  • Homepage

    Publication
    Dec. 23, 2007
    Citations: 27
    65 VIRmiRNA VIRmiRNA is the first specialized resource of experimentally proven virus-encoded miRNAs and their associated targets.
  • viruses
  • miRNA basic information
  • target experimental
  • predicted target
  • diseases/pathways
  • Homepage

    Publication
    Nov. 7, 2014
    Citations: 19
    66 ViTa ViTa is a database which collects virus data from miRBase and ICTV, VirGne, VBRC, etc, including known miRNAs on virus and supporting predicted host miRNA targets by miRanda and TargetScan. ViTa also provide effective annotations, including human miRNA expression, virus infected tissues, annotation of virus and comparisons.
  • human
  • mouse
  • rat
  • chicken
  • viruses
  • target experimental
  • predicted target
  • literature mining
  • miRNA expression
  • Homepage

    Publication
    Jan. 3, 2007
    Citations: 32
    67 YM500v2 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.
  • human
  • miRNA basic information
  • predicted target
  • diseases/pathways
  • miRNA expression
  • Homepage

    Publication
    Nov. 14, 2014
    Citations: 17