| 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. |
| 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 |
| Target prediction correlated with expression data |
| 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. |
| 121 cell lines linked to miRNA investigations 556 organs connected to miRNA studies |
| Composite target prediction Experimentally validated miRNA targets miRNA roles in diseases miRNA interactions in pathways |
| 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. |
| Including expression profile of different miRNAs in various tissues and cancers Viewing multiple tissues in one search page |
| Single resource target prediction |
| 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. |
| MicroRNAs which are derived from transposable elements (TEs) either transcriptionally or structurally |
| 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. |
| miREnvironment integrated >2500 entries including 800 miRNAs, 260 experimental factors, 180 phenotypes from 17 species |
| 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. |
| Expression profile of tissues, organs and cell lines Including deep sequencing data as principal resources on microRNA diversity and expression |
| Composite target prediction miRNA functions miRNA interactions in pathways |
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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. |
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Both known and predicted miRNAs |
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miRNA sequence and annotation |
| 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. |
Containing various data sets including different cancer types
| Composite target prediction miRNA function |
| 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 . |
| Expression profiles of 224 human miRNAs in 18 major normal tissues in human |
| Composite target prediction |
| 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. |
| The expression patterns were generated by RNA in situ hybridization (ISH) |
| 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. |
| Comparison of different samples Comparison of different sets of samples Clustering of MiRNA Expression Profiles |
| 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. |
| Examine influence of small RNAs on expression profiles |
| 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. |
| Isomir identification Arm switching discovery and novel miRNA prediction from small RNA sequencing |
| miRNA roles in diseases |
| DIANA-miRGen v3.0 provides the 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. To this end, more than 7.3 billion RNA-, ChIP- and DNase-Seq next generation sequencing reads were analyzed/assembled and combined with state-of-the-art miRNA TSS prediction and TF binding site identification algorithms. |
| Search by miRNA or TF name |
| CircuitsDB 2 is an improvement and extension of our previous work, CircuitsDB, in which we systematically study, by computational means, the combined role of microRNAs and lncRNAs within the human regulatory network and their impact on cancer-related genes. CircuitsDB 2 contains a large number of regulatory circuits, composed by Transcription Factors, target genes, microRNAs and lincRNAs interacting together, in the human genome. |
| Combined role of microRNAs and lncRNAs within the human regulatory network Regulatory circuits, composed by Transcription Factors, target genes, microRNAs and lncRNAs interacting together |
| miReg is a manually curated microRNA Regulation Resource that represents regulatory relationships among validated upstream regulators (Transcription factors or TFs, drugs, physical, and chemical), downstream targets, associated biological process, experimental condition or disease state, and up/down regulation of the miR in that condition in a graphical and user friendly manner along with corresponding published references. |
| Containing validated upstream regulators as transcription factor, drug, physical, and chemical |
| MIR@NT@N is an effective computational approach to identify novel molecular regulations and to predict gene regulatory networks and sub-networks including conserved motifs within a given biological context. MIR@NT@N uses a graph-based approach to predict novel molecular actors across multiple regulatory processes (i.e. TFs acting on protein-coding or miRNA genes, or miRNAs acting on messenger RNAs). Exploiting these predictions, the user can generate networks and further analyze them to identify sub-networks, including motifs such as feedback and feedforward loops. |
| Provides a user-friendly graph-based application connected to a large scale database |
| miRStart is a novel resource of human microRNA TSSs (transcription start sites), systematically incorporates significant datasets derived from TSS-relevant experiments to identify transcription start sites of microRNAs. The distribution patterns of these experimental features within 50 k upstream region of microRNA precursors provides an insight into determining reliable microRNA TSSs. |
| Systematically incorporates datasets to identify transcription start sites of microRNAs |
| miRT is a novel database of validated miRNA TSSs prepared by collecting data from several experimental studies that validate miRNA TSSs and are available for full download. miRT is a web server and it is also possible to convert the TSS loci between different genome built. miRT might be a valuable resource for advanced research on miRNA regulation. |
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Search by miRNA name |
| PMMR constructed the miRNA and TF induced regulatory network for humans by combining all possible regulations between miRNAs and TFs. Topological analysis of the network revealed some of its non-trivial and intrinsic properties. The concept of topological overlap has been extended to formulate a novel dissimilarity measure that is capable of mining groups of closely interacting molecules from a weighted digraph such that the molecules in each group regulate each other to a large extent. Many of the identified TF modules are found to be enriched in different functional categories or displayed significant associations with common diseases. |
| Showing regulated and regulating miRNAs |
| PuTmiR provides an important resource for analyzing the direct and indirect regulation of human miRNAs. While it is already an established fact that miRNAs are regulated by TFs binding to their USR, this database might possibly help to study whether a miRNA can also be regulated by the TFs binding to their downstream region. |
| In 10 kb or custom regions Searching upstream or downstream reigons |
| RegRNA is an integrated web server for identifying the homologs of regulatory RNA motifs and elements against an input mRNA sequence. Both sequence homologs and structural homologs of regulatory RNA motifs can be recognized. |
| Sequence homologs or structural homologs of regulatory RNA motifs can be identified |
| TransmiR contains TFs and miRNAs with regulatory pairs between TFs and miRNAs. TransmiR included references to the published literature (PubMed ID) information about the organism in which the relationship was found, whether the TFs and miRNAs are involved with tumors, miRNA function annotation and miRNA-associated disease annotation. TransmiR provides a user-friendly interface by which interested parties can easily retrieve TF–miRNA regulatory pairs by searching for either a miRNA or a TF. |
| Including 735 entries, which include 201 TFs, 209 miRNAs, 16 organisms |
| RegRNA 2.0 is an integrated web server for identifying functional RNA motifs in an input RNA sequence. RegRNA 2.0 extends our previvous work, RegRNA which is a widely used regulatory RNA motifs identification tool by incoporating more analytical methods and updated data sources. Through our integrated user-friendly interface, user can conveniently use these analytical approaches and observe results with good graphical visualization. |
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Functional RNA motifs in an input RNA sequence |
| 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. |
| Select and compare groups of microRNA or mRNA expression samples from the extensive DIANA expression database |
| miRNA gene regulation |
| 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. |
| Containing miRNA:mRNA, TF:mRNA and TF:miRNA interactions derived from extensive experimental data sets Including 450 000 miRNA interactions and 2 000 000 TF binding sites from specific or high-throughput techniques |
| miRNA expression |
| 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. |
| miRNA-disease associations along with expression pattern and number of articles Network visualize miRNA body fluid associations |
| 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. |
| 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 |
| 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. |
| Extracellular/Circulating non-coding RNAs |
| 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. |
| MicroRNAs from wild-type and mutant plants Based on quantitative Real Time PCR and sequencing experiments |
| 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. |
| MicroRNA deregulation following exposure to different stress stimuli |
| 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. |
| The most comprehensive comparative view of plant miRNA expression In multiple tissues and developmental stages |
| 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. |
| Provides information on query function of plant miRNAs and their target sequences, gene ontology, and differential expression profiles |
| 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. |
| Experimentally validated small molecules' effects on microRNA expression Search by miRNA or small molecule |
| 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. |
| Assesses miRNA signatures from publicly available miRNA profiles |
| EpimiR database collects 1974 regulations between 19 kinds of epigenetic modifications (such as DNA methylation, histone acetylation, H3K4me3, H3S10p) and 617 miRNAs across seven species (including Homo sapiens, Mus musculus, Rattus norvegicus, Gallus gallus, Epstein-Barr virus, Canis familiaris and Arabidopsis thaliana) from >300 references in the literature. These regulations can be divided into two parts: miR2Epi (103 entries describing how miRNA regulates epigenetic modification) and Epi2miR (1871 entries describing how epigenetic modification affects miRNA). |
| miRNA regulated by epigenetics miRNA regulating epigenetics Search by miRNA or epigenetics |
| microPIR2 provides approximately 80 million human and 40 million mouse predicted target sites. microPIR2 is a tool for comparative analysis of target sites on the promoters of human-mouse orthologous genes. In particular, this new feature was designed to identify potential microRNA-promoter interactions conserved between species that could be stronger candidates for further experimental validation. microPIR2 includes nuclear and cytoplasmic localization of microRNAs and miRNA-disease association. |
| Search by gene, miRNA, disease or phenotype |
| TMREC integrated curated transcriptional and post-transcriptional regulations to construct the TF and miRNA regulatory network. Next, this database identified all linear paths using the Breadth First Search traversal method. Finally, we used known disease-related genes and miRNAs to measure the strength of association between cascades and diseases. Currently, TMREC consists of 74,248 cascades and 25,194 cascade clusters, involving in 412 TFs, 266 miRNAs and 545 diseases. |
| Understand the transcriptional and post-transcriptional regulatory mechanisms in specific disease Identify the potential therapeutic targets in the upstream of the cascades |
