The miRBase database is a searchable database of published miRNA sequences and annotation. Each entry in the miRBase Sequence database 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. All sequence and annotation data are also available for download.
An easy-to-use online database that keeps track of all historical and current miRNA annotation present in the miRBase database.
FirePlex Discovery Engine
The FirePlex Discovery Engine assembles a list of the most important microRNAs and associated genes from the scientific literature for any keyword or topic, putting years of research at your fingertips in seconds.
miROrtho contains predictions of precursor miRNA genes covering several animal genomes combining orthology and a Support Vector Machine. It provides homology extended alignments of already known miRBase families and putative miRNA families.
DIANA-TarBase v8.0 is a reference database devoted to the indexing of experimentally supported microRNA (miRNA) targets. Its eighth version is the first database indexing >1 million entries, corresponding to ∼670 000 unique miRNA-target pairs. The interactions are supported by >33 experimental methodologies, applied to ∼600 cell types/tissues under ∼451 experimental conditions. It integrates information on cell-type specific miRNA-gene regulation, while hundreds of thousands of miRNA-binding locations are reported.
miRCancer : microRNA Cancer Association Database
miRCancer provides comprehensive collection of microRNA (miRNA) expression profiles in various human cancers which are automatically extracted from published literatures in PubMed. Search by cancer names or the on-site sequence analysis tools is possible.
The new version of miRWalk stores predicted data obtained with a maschine learning algorithm including experimentally verified miRNA-target interactions. The focus lies on accuracy, simplicity, user-friendly design and mostly up to date informations.
omiRas provides an interface to generate a miRNA-mRNA interaction network for user selected microRNAs. Interactions between genes and miRNAs are determined by the interesection of 7 databases (TargetScan, miRanda, PICTAR, PITA, miRDB, TarBase, miRConnect).
microRNA deep sequencing tools
miRDeep2 is a completely overhauled tool which discovers microRNA genes by analyzing sequenced RNAs.
miRNAkey is a software package designed to be used as a base-station for the analysis of miRNA deep sequencing data.
microRNA data analyses tools
This web tool allows users to upload their own data and easily create Principal Component Analysis (PCA) plots and heatmaps.
An interactive tool for comparing lists using Venn Diagrams with support for up to 4 sets.
Tools4miRs is a first, manually curated platform gathering at the present over 170 methods for the broadly-defined miRNA analysis. All tools in Tools4miRs are classified in the four general and seven more detailed categories. In each of the aforementioned sections user can additionally filter available methods according to his research needs, capabilities and preferences.
Human miRNA Tissue Atlas
TissueAtlas allows identifying the tissues of origin of miRNAs and provides insights into specificity and heterogeneity of miRNAs with respect to tissues.
Rat miRNA Tissue Atlas
RATEmiRs is a database of rat microRNA-Seq data in several tissues. “Data Driven” pipelines are available to detect tissue-specific and tissue-enriched microRNAs. “User Driven” entrez is available to enter a list of IDs of mature microRNAs. Organ-specific pipelines detects microRNAs that are specific for a particular set of tissues that comprise of an organ.
GeneCards is a searchable, integrative database that provides comprehensive, user-friendly information on all annotated and predicted human genes. It automatically integrates gene-centric data from ~125 web sources, including genomic, transcriptomic, proteomic, genetic, clinical and functional information.
The GeneCards Suite of Databases
- MalaCards: A database of human maladies and their annotations
- PathCards: The integrated database of human pathways and their annotations
- GeneALaCart: Generates a file of GeneCards annotations for your list of genes
- GeneLoc: Presents an integrated map for each human chromosome, based on data integrated by the GeneLoc algorithm
A comprehensive reference dataset of detailed miRNA expression profiles from seven types of human peripheral blood cells, serum, exosomes and whole blood. The overall dataset was generated from 450 small RNA libraries using high-throughput sequencing.