| # | Name | Description | Organism Specific |
Data Collection | Data AvailableFor Download | References |
|---|---|---|---|---|---|---|
| 1 | ADmiRE | Annotative Database of miRNA Elements is a miRNA variant annotation tool which combines miRNA sequence features derived from conservation and variation with biologically important annotations. Framework for microRNA variant annotation and prioritization using human population and disease datasets. | Homepage Publication Oct. 10, 2018 Citations: 13 | |||
| 2 | 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. | Homepage Publication Oct. 6, 2008 Citations: 13 | |||
| 3 | CREAM | CREAM (Chemotherapy ResistancE-Associated MiRSNP Database) is a free online database depositing the functional miRSNP associated with chemotherapy resistance. | Homepage Publication May 29, 2014 Citations: 3 | |||
| 4 | dbDEMC 3.0 | 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. | Homepage Publication Jan. 4, 2017 Citations: 152 | |||
| 5 | 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. | Homepage Publication Nov. 26, 2015 Citations: 394 | |||
| 6 | 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 | Homepage Publication Nov. 21, 2014 Citations: 412 | |||
| 7 | 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. | Homepage Publication Jan. 8, 2016 Citations: 26 | |||
| 8 | 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. | Homepage Publication Jan. 6, 2015 Citations: 9 | |||
| 9 | ExoCarta | ExoCarta, an exosome database, provides with the contents that were identified in exosomes in multiple organisms. | Homepage Publication Feb. 22, 2016 Citations: 735 | |||
| 10 | 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. | Homepage Publication Nov. 4, 2013 Citations: 365 | |||
| 11 | 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. | Homepage Publication March 22, 2011 Citations: 32 | |||
| 12 | IsomiR Bank | IsomiR Bank is the integrative resource that contains the sequence and expression of isomiRs. | Homepage Publication July 1, 2016 Citations: 25 | |||
| 13 | 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. | Homepage Publication Dec. 22, 2010 Citations: 14 | |||
| 14 | 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. | Homepage Publication Feb. 13, 2012 Citations: 42 | |||
| 15 | 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. | Homepage Publication Jan. 1, 2009 Citations: 662 | |||
| 16 | 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. | Homepage Publication Oct. 19, 2012 Citations: 84 | |||
| 17 | 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. | Homepage Publication Nov. 25, 2013 Citations: 2683 | |||
| 18 | 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. | Homepage Publication Aug. 24, 2014 Citations: 48 | |||
| 19 | 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. | Homepage Publication Jan. 16, 2013 Citations: 239 | |||
| 20 | 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. | Homepage Publication Nov. 5, 2014 Citations: 1027 | |||
| 21 | 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. | Homepage Publication Jan. 1, 2009 Citations: 763 | |||
| 22 | 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. | Homepage Publication June 16, 2015 Citations: 37 | |||
| 23 | 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. | Homepage Publication Nov. 27, 2012 Citations: 81 | |||
| 24 | 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. | Homepage Publication Nov. 19, 2015 Citations: 32 | |||
| 25 | 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 | Homepage Publication Sept. 1, 2015 Citations: 300 | |||
| 26 | miRNA - Target Gene Prediction at EMBL | This database provides access to the 2003 and 2005 miRNA-Target predictions for Drosophila miRNAs. | Homepage Publication Feb. 15, 2005 Citations: 1025 | |||
| 27 | 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. | Homepage Publication Nov. 15, 2013 Citations: 26 | |||
| 28 | 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. | Homepage Publication Jan. 1, 2009 Citations: 42 | |||
| 29 | 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. | Homepage Publication Oct. 13, 2016 Citations: 67 | |||
| 30 | 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. | Homepage Publication Dec. 20, 2014 Citations: 12 | |||
| 31 | miRStress | The miRStress database is a comprehensive resource that documents microRNA deregulation following exposure to different stress stimuli. | Homepage Publication Nov. 14, 2013 Citations: 15 | |||
| 32 | 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. | Homepage Publication Aug. 1, 2012 Citations: 167 | |||
| 33 | 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. | Homepage Publication Nov. 20, 2015 Citations: 570 | |||
| 34 | miRWalk | A publicly available comprehensive resource, hosting the predicted as well as the experimentally validated microRNA (miRNA)-target interaction pairs. | Homepage Publication July 30, 2015 Citations: 736 | |||
| 35 | 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. | Homepage Publication Oct. 1, 2015 Citations: 22 | |||
| 36 | 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. | Homepage Publication July 24, 2014 Citations: 363 | |||
| 37 | OncomiR | OncomiR is an online resource for exploring miRNA dysregulation in cancer. | Homepage Publication Feb. 15, 2018 Citations: 103 | |||
| 38 | 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. | Homepage Publication March 20, 2014 Citations: 65 | |||
| 39 | 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. | Homepage Publication Jan. 15, 2014 Citations: 6 | |||
| 40 | 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. | Homepage Publication March 1, 2013 Citations: 32 | |||
| 41 | 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. | Homepage Publication Jan. 20, 2010 Citations: 126 | |||
| 42 | PmiREN | The Plant miRNA Encyclopedia (PmiREN) is a comprehensive plant repository that contains approximately 39 700 miRNA sequences from 179 different plant species. According to the latest release of PmiREN (v2.0), the database contains an extensive collection of over 38000 miRNA sequences from 179 different species including model plants and major agricultural crops. PmiREN allows users to explore detailed information on discovered and annotated miRNAs. This includes data such as genomic location, miRNA expression profiles, secondary structures of hairpin precursors, miRNA targets that have been predicted using advanced bioinformatics tools and relevant information of miRNA conservation in diverse plant species. | Homepage Publication Sept. 23, 2021 Citations: 41 | |||
| 43 | 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. | Homepage Publication April 13, 2016 Citations: 17 | |||
| 44 | 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. | Homepage Publication June 3, 2013 Citations: 15 | |||
| 45 | 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. | Homepage Publication Nov. 14, 2014 Citations: 90 | |||
| 46 | 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. | Homepage Publication Oct. 24, 2013 Citations: 161 | |||
| 47 | PuTmiR | Focus on TF to miRNA regulation and provide a novel interface for extracting the list of putative TFs for human miRNAs. | Homepage Publication April 15, 2010 Citations: 27 | |||
| 48 | Rfam 14.9 | Rfam is the database of non-coding RNA (ncRNA) families (1), each represented by a multiple sequence alignment (known as the seed), a consensus secondary structure, and a covariance model to annotate non-coding RNAs in nucleotide datasets using the Infernal software. | Homepage Publication Jan. 8, 2021 Citations: 468 | |||
| 49 | RNA central | RNAcentral is recognized as comprehensive database, providing access to an extensive collection over 18 million non-coding RNA (ncRNA) sequences derived from different species . The RNAcentral database has recently integrated secondary (2D) structure information for over 13 million sequences, establishing RNAcentral as the world's largest repository for RNA 2D structures. RNAcentral has compiled a comprehensive catalog of ncRNA data, including sequence similarity search, detailed ncRNA annotations. At present, the RNAcentral comprises 59 Expert Databases, including miRBase, Ensembl Plants, Rfam, TAIR etc | Homepage Publication Jan. 8, 2021 Citations: 153 | |||
| 50 | SM2miR | SM2miR: a database of the experimentally validated small molecules’ effects on microRNA expression | Homepage Publication Feb. 1, 2013 Citations: 102 | |||
| 51 | 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 | Homepage Publication Nov. 17, 2015 Citations: 69 | |||
| 52 | 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. | Homepage Publication Dec. 1, 2013 Citations: 2920 | |||
| 53 | 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. | Homepage Publication Sept. 6, 2013 Citations: 10 | |||
| 54 | TissueAtlas | small noncoding RNA tissue atlas determining the RNA expression for nine different types of sncRNAs. | Homepage Publication May 5, 2016 Citations: 535 | |||
| 55 | 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. | Homepage Publication May 1, 2015 Citations: 12 | |||
| 56 | TransmiR | A database for transcription factor-microRNA regulations. | Homepage Publication Sept. 28, 2009 Citations: 218 | |||
| 57 | Vir-Mir db | Vir-Mir database, a database containing predicted viral miRNA candidate hairpins. | Homepage Publication Dec. 23, 2007 Citations: 35 | |||
| 58 | VIRmiRNA | VIRmiRNA is the first specialized resource of experimentally proven virus-encoded miRNAs and their associated targets. | Homepage Publication Nov. 7, 2014 Citations: 60 | |||
| 59 | 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. | Homepage Publication Jan. 3, 2007 Citations: 49 | |||
| 60 | 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. | Homepage Publication Nov. 14, 2014 Citations: 34 |
