MicroRNA databases | Non-coding transcript data analysis
MicroRNAs (miRNAs) are small non-coding RNA (∼22 nt) involved in the post-transcriptional regulation of gene expression. miRNAs promote the degradation or inhibit the expression of messenger RNA by binding to specific sequences generally located in the 3′ UTR of their target.
Provides a collection of noncoding RNA sequences. Rfam is an online resource where RNA sequences are grouped into “families” and “clans” on the basis of nucleotide sequence and secondary structure homology. It includes many different types of ncRNA genes, cisregulatory elements and intronic elements, all annotated in as many species as possible. This database is searched for homologous sequences.
Provides an integrated expression collection of miRNAs and their promoters. The database contains matching Cap Analysis Gene Expression (CAGE) data from 396 human and 47 mouse RNA samples. It offers promoters for about 1,300 human and 800 mouse miRNAs. This atlas can conserve strong sequence between human and mouse species. It is a part of the FANTOM5 database.
Permits users to identify and annotate long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs), and to predict the functions of lncRNAs. deepBase is a database that facilitates the display and the annotation and discovery of small RNAs (sRNAs), lncRNAs and circRNAs. It also provides expression and evolution profiles of lncRNAs, circRNAs and small RNAs. Two web-based tools, lncSeeker and lncFunction, can be used to identify high-confidence lncRNAs, and to predict lncRNA functions.
Provides a genome-wide map of transcription factor-microRNA (TF–miRNA) interactions for multiple tissues and cell-lines in Homo sapiens and Mus musculus. miRGen is a repository that supports miRBase and Ensembl nomenclatures, allowing for any combination of pre-miRNA and TF names as valid search terms for querying the database. The database provides several search and filtering options, such as combinations of pre-miRNA/TF names, the supported tissues and cell lines, or a threshold of the expression value for each TF.
Provides a collection of miRNA-associated diseases, obtained by manual curation from literature data. HMDD furnishes detailed 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. This database is useful for predicting functions and environmental factor-disease relationships.
Distributes published microRNA sequences, for browsing and searching by sequence and keywords. miRBase is a public repository for all published microRNA sequences and associated annotation. For each microRNA sequence entry, this online resource provides the primary references that describe its discovery, links to the evidence supporting the microRNA annotation, genomic coordinates and links to databases of predicted and validated microRNA target sites.
Collects ncRNA sequences from a broad range of species. RNAcentral gives access to data, search functionality, cross-references, source code and an integrated genome browser for selected species. It integrates genomic locations for sequences in selected model organisms, quality control information for all sequences, functional and structural annotations, and miRNA targets. This platform can assist users to discover the correct miRNA identifier.
Focuses in post-transcriptional regulation which integrates information related to binding site data between RNA binding proteins (RBPs) and microRNAs. To enable the inclusion of doRiNA into third-party analysis pipelines, all operations are accessible via a REST API. Alternatively, local installations can be queried using a Python API.
Consists of a database of plant and animal microRNAs. miRNEST is an online resource concerning plant, animal and virus miRNAs that contains information concerning over 18000 pre-miRNAs in 21 plant and animal species. It also stores miRNA splice sites information. Moreover, target predictions for miRNAs from 10 species are supported by degradome data.
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). We expanded the scope of the database by including somatic mutations that impact the interactions between miRNAs and two classes of non-coding RNAs, circRNAs and lncRNAs. A recently developed webserver, miR2GO, was integrated with the database to provide a seamless pipeline for assessing functional impacts of somatic mutations in miRNA seed regions. Data and functions from multiple sources including biological pathways and genome-wide association studies were updated and integrated with SomamiR 2.0 to make it a better platform for functional analysis of somatic mutations altering miRNA-ceRNA interactions.
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.
Deals with literature-curated transcription factors (TF)-miRNA regulation data about more than 15 organisms. TransmiR is a repository built around three main features: (i) database query, which can be searched by name of either a TF or a mirna , (ii) network visualization, to display data of interest as a network diagram; and (iii) enrichment analysis, allowing the retrieving of overrepresenting TFs.
Supplies a repository of interactions between miRNA and target pathways. MiRPathDB collects single miRNA that regulate pathways, gene ontologies and other categories. This database associates each miRNA with five target sets and pre-computed enrichment analyses. It allows the comparison between human target pathways and Mus musculus data and the visualization of heat maps for pathway databases.
An integrated resource to analyze signaling pathway cross-talks, miRNAs and regulatory enzymes in zebrafish. SignaFish contains more than 200 curation-based signaling interactions, 132 further interactions listed in other resources, and it also lists potential miRNA-based regulatory connections for seven major signaling pathways. From the SignaFish website, users can reach other web resources, such as ZFIN. SignaFish provides signaling or signaling-related interactions that can be examined for each gene or downloaded for each signaling pathway. SignaFish serves as a navigating point for experimental design and evaluation for the zebrafish community and for researchers focusing on nonmodel fish species, such as cyclids.
A comprehensive bioinformatics resource to archive non-coding RNA (ncRNA)-associated cell death interactions. ncRDeathDB documents a total of more than 4600 ncRNA-mediated programmed cell death (PCD) entries in 12 species. ncRDeathDB provides a user-friendly interface to query, browse and manipulate these ncRNA-associated cell death interactions. Furthermore, this resource will help to visualize and navigate current knowledge of the noncoding RNA component of cell death and autophagy, to uncover the generic organizing principles of ncRNA-associated cell death systems, and to generate valuable biological hypotheses.
Allows exploration of associations between ncRNAs and diseases. MNDR integrates manual literature curation, experimental resources and prediction algorithms. It contains a confidence score for each ncRNA–disease association and mapping disease names to the Disease Ontology and to the MeSH. The database gathers about 8 800 experimental lncRNA-associated, 70 400 experimental miRNA-associated, 120 experimental piRNA-associated and 70 experimental snoRNA-associated entries.
Deals with human small non-coding RNAs (sncRNA) genes and mature sncRNA products. DASHR allows users to: (i) retrieves annotation; (ii) visualize expression data sncRNA loci, expression and annotation data as UCSC genome browser tracks; (iii) search for and compare both expression and processing information; Its annotation and expression data encompass the major classes of sncRNAs, including microRNAs (miRNAs), Piwi-interacting (piRNAs), cytoplasmic or ribosomal RNAs (rRNAs).
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 manual literature curation. As the largest known collection of experimental validated miRNA targets, it emphasizes systematic and structured documentation of experimental support of miRNA–target interactions. This database not only serves the experimental researchers by providing the lists of confirmed targets of the miRNAs of their interest, but also provides a large and high-quality dataset that will facilitate the development of the next-generation miRNA target prediction programs. The Predicted Targets component of miRecords is an integration of predicted miRNA targets produced by 11 established miRNA target prediction programs. As the most complete integration of predicted miRNA targets, it is expected to provide considerable help to researchers investigating new miRNA targets.
Provides a comprehensive platform for the exploration of microRNA expression data based on quantitative Real Time polymerase chain reaction (PCR) and next generation sequencing (NGS) sequencing experiments, covering various developmental stages, from wild-type to mutant plants. The mirEX 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. In total, the database contains information about the expression of 461 miRNAs representing 268 families. The data can be explored through the use of advanced web tools, including (i) a graphical query builder system allowing a combination of any given species, developmental stages and tissues, (ii) a modular presentation of the results in the form of thematic windows, and (iii) a number of user-friendly utilities such as a community-building discussion system and extensive tutorial documentation. All data contained within the mirEX database can be downloaded for use in further applications in a context-based way from the result windows or from a dedicated web page.
Offers a repository for miRNA deregulation in various human diseases. miR2Disease provides an interface where users can query the database through microRNA ID, disease name or target gene. This database has a fuzzy search function which, combined with a controlled disease vocabulary, permits to retrieve relevant microRNA–disease relationship information. Il allows users to submit established microRNA-disease relationships that are not documented.