| The predicted miRNA functions are accessible in the miRNA bodymap. Predicted miRNA functions were either validated experimentally or compared to published data. Functional miRNA annotations based on target prediction. Using the miRNA2function tool, predicted miRNA functions for your miRNA of choice can be retrieved. The function2miRNA tool works the other way around and allows users to select a function of interest and retrieve miRNAs associated with it. |
| Detection miRNAs, genes and TF interactions Search by miRNA or function entry Search for lncRNAs functions |
| Composite target prediction miRNA expression |
| FAME use computational target predictions in order to automatically infer the processes affected by human miRNAs. Our approach improves upon standard statistical tools by addressing specific characteristics of miRNA regulation. Our analysis is based on a novel compendium of experimentally verified miRNA-pathway and miRNA-process associations that we constructed, which can be a useful resource by itself. Our method also predicts novel miRNA-regulated pathways, refines the annotation of miRNAs for which only crude functions are known, and assigns differential functions to miRNAs with closely related sequences. |
| Use computational target predictions to infer the processes affected by miRNAs Assigns differential functions to miRNAs |
| GOmir is a novel stand-alone application consisting of two separate tools: JTarget and TAGGO. JTarget integrates miRNA target prediction and functional analysis by combining the predicted target genes from TargetScan, miRanda, RNAhybrid and PicTar computational tools as well as the experimentally supported targets from TarBase and also providing a full gene description and functional analysis for each target gene. On the other hand, TAGGO application is designed to automatically group gene ontology annotations, taking advantage of the Gene Ontology (GO), in order to extract the main attributes of sets of proteins. |
| Integrate microRNA target prediction and functional analysis |
| miRGator v3.0 compiled the deep sequencing miRNA data available in public and implemented several novel tools to facilitate exploration of massive data. miRNA–target relation is essential for understanding miRNA function. Coexpression analysis of miRNA and target mRNAs, based on miRNA-seq and RNA-seq data from the same sample, is visualized in the heat-map and network views where users can investigate the inverse correlation of gene expression and target relations, compiled from various databases of predicted and validated targets. |
| Containing TFs, genes and miRNAs and their interactions Coexpression analysis of miRNA and target mRNAs, based on miRNA-seq and RNA-seq data from the same sample |
| Composite target prediction miRNA expression miRNA interactions in pathways |
| miRò is a web-based knowledge base that provides users with miRNA-phenotype associations in humans. It integrates data from various online sources, such as databases of miRNAs, ontologies, diseases and targets, into a unified database equipped with an intuitive and flexible query interface and data mining facilities. The main goal of miRò analysis through sophisticated mining techniques and the introduction of a new layer of associations between genes and phenotypes inferred based on miRNAs annotations. |
| miRNA functional annotations inferred through their validated and predicted targets Based on miRanda, PicTar, TargetScan and miRecords algorithms Measures the pairwise functional similarity of the given miRNAs |
| Composite target prediction miRNA roles in diseases |
| MISIM infers the pairwise functional similarity and functional network for human miRNAs based on the structures of their disease relationships. Comparisons showed that the calculated miRNA functional similarity is well associated with prior knowledge of miRNA functional relationship. More importantly, this method can also be used to predict novel miRNA biomarkers and to infer novel potential functions or associated diseases for miRNAs. In addition, this method can be easily extended to other species when sufficient miRNA-associated disease data are available for specific species. |
| Generation of a miRNA functional network |
| "TAM can efficiently identify meaningful categories for given miRNAs and can be used to identify novel miRNA biomarkers. TAM integrated miRNAs into various meaningful categories according to prior knowledge, such as miRNA family, miRNA cluster, miRNA function, miRNA associated diseases, and tissue specificity. Using TAM, given lists of miRNAs can be rapidly annotated and summarized according to the integrated miRNA categorical data. Moreover, given a list of miRNAs, TAM can be used to predict novel related miRNAs. |
| Identify categories for given miRNAs Identify novel miRNA biomarkers |
| UCbase & miRfunc provides ultraconserved sequences data and shows miRNA function. Also, it links UCRs and miRNAs with the related human disorders and genomic properties. |
| Link ultraconserved sequences and miRNAs with the related human disorders and genomic properties |
| miR2Disease, a manually curated database, aims at providing a comprehensive resource of microRNA deregulation in various human diseases. Around one-seventh of the microRNA-disease relationships represent the pathogenic roles of deregulated microRNA in human disease. Each entry in the miR2Disease contains detailed information on a microRNA-disease relationship, including a microRNA ID, the disease name, a brief description of the microRNA-disease relationship, an expression pattern of the microRNA, the detection method for microRNA expression, experimentally verified target gene(s) of the microRNA and a literature reference. |
| Search by miRNA ID, disease name or target gene. |
| HMDD the Human microRNA Disease Database is a database that curated experiment-supported evidence for human microRNA and disease associations. Each entry in HMDD v1.0 has four items for annotation; they are miRNA name, disease name, the reference PubMed ID, and the evidence supporting the miRNA-association from the original paper. |
| Contain miRNA names, disease names, dysfunction evidences, and the literature PubMed ID |
| CAMi-Finder is a resource for human cancer miRNA associations. It provides two types of functionalities: first, Showing all the validated cancer-miRNA relationship with a mouse-click and second, Predicts novel cancer-miRNA relationships by mining predicted miRNA-target genes Targetminer, TargetScan, miRanda , PITA and TargetSpy. |
| Search by cancer type or miRNA Mining of customized associations between cancer causing microRNAs |
| "dbDEMC is expected to be a valuable source for identification of cancer-related miRNAs, thereby helping with the improvement of classification, diagnosis and treatment of human cancers. This database collected the miRNA expression profiles of 14 cancer types, curated from 48 microarray data sets in peer-reviewed publications. The Significance Analysis of Microarrays method was used to retrieve the miRNAs that have dramatically different expression levels in cancers when compared to normal tissues. A total of 607 differentially expressed miRNAs (590 mature miRNAs and 17 precursor miRNAs) were obtained in the current version of dbDEMC. |
| Search by miRNA ID |
| miRdSNP is a database of manually curated dSNPs on the 3'UTRs of human genes from available publications in PubMedThe 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. The web interface displays detailed sequence views showing the relationship between dSNPs, miRNA target sites, and SNPs. An interactive visualization tool shows the chromosomal distribution of dSNPs, miRNA target sites (from TargetScan), and SNPs. |
| Disease-associated SNPs and miRNA target sites on 3′UTRs of mRNAs |
| miRò is a web-based knowledge base that provides users with miRNA-phenotype associations in humans. It integrates data from various online sources, such as databases of miRNAs, ontologies, diseases and targets, into a unified database equipped with an intuitive and flexible query interface and data mining facilities. The main goal of miRò analysis through sophisticated mining techniques and the introduction of a new layer of associations between genes and phenotypes inferred based on miRNAs annotations. |
| miRNA relations to disease concluded from their validated and predicted targets Based on miRanda, PicTar, TargetScan and miRecords algorithms |
| Composite target prediction miRNA function |
| The microRNA-gene association database miRSel combines text-mining results with existing databases and computational predictions. Text mining enables the reliable extraction of microRNA, gene and protein occurrences as well as their relationships from texts. Thereby, we increased the number of human, mouse and rat miRNA-gene associations by at least three-fold as compared to e.g. TarBase, a resource for miRNA-gene associations. |
| Extracting associations between miRNAs and genes from the biomedical literatures |
| miRTRAP incorporates the mechanisms of miR biogenesis and includes additional criteria regarding the prevalence and quality of small RNAs arising from the antisense strand and neighboring loci. This program was applied to the simple chordate Ciona intestinalis and identified nearly 400 putative miR loci. |
| Functional analyses of disease-related miRNAs from high throughput sequencing data |
| miRWalk2.0 is supplying the biggest available collection of predicted and experimentally verified miRNA-target interactions with various novel and unique features. Information on miRNA-target interactions on 2,035 disease ontologies, 6,727 Human Phenotype ontologies and 4,980 OMIM disorders is available. |
| Based on predicted and validated results 98,887 relationships on 1572 miRNAs from human, mouse and rat linked to 691 diseases |
| Composite target prediction Experimentally validated miRNA targets miRNA expression miRNA interactions in pathways |
| MMIAs is microRNA and mRNA integrated analysis that integrates microRNA and mRNA expression data with predicted microRNA target information for analyzing microRNA-associated phenotypes and biological functions. To assign biological relevance to the integrated microRNA/mRNA profiles, MMIA uses exhaustive human genome coverage, including various disease-associated genes as well as conventional canonical pathways and Gene Ontology. |
| Biological and pathological causes and effects of the expression Using TargetScan, PITA and PicTar algorithms |
| Target prediction correlated with expression data |
| 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 PhenomiR database provides data from 542 studies that investigate deregulation of microRNA expression in diseases and biological processes as a systematic, manually curated resource. Using the PhenomiR dataset, depending on disease type, independent information from cell culture studies contrasts with conclusions drawn from patient studies. |
| Differentially expressed miRNAs in biological processes and diseases |
| Polymorphisms in microRNAs and their target sites (PolymiRTS) are known to disrupt miRNA function, leading to the development of disease and variation in physiological and behavioral phenotypes. PolymiRTS database is an integrated platform for analyzing the functional impact of genetic polymorphisms in miRNA seed regions and miRNA target sites. Recent advances in genomic technologies have made it possible to identify miRNA-mRNA binding sites from direct mapping experiments such as CLASH (cross linking, ligation and sequencing of hybrids). |
| Relating microRNA and target sites polymorphisms to diseases and traits |
| Sarcoma microRNA Expression Database S-MED is a repository that describes the patterns of miRNA expression in various human sarcoma types. S-MED provides both basic and advanced data search options for exploration of the data in heat map and text/numerical formats. The database also provides statistical details such as fold changes and P-values for differentially expressed miRNAs in each sarcoma type and corresponding normal tissue. |
| SExpression profiles for over 300 tumor tissue samples representing 22 different sarcoma types |
| SomamiR 2.0 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). 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. |
| determine the effect of somatic mutations on miRNA function in cancer Somatic mutations in miRNA or miRNA target site |
| Human microRNA Disease Database, HMDD v2.0, is a collection of experimentally supported human microRNA and disease associations. In the updated database, miRNA-disease association data were annotated in more details. For example, miRNA-disease association data from genetics, epigenetics, circulating miRNAs and miRNA-target interactions were integrated into the database. In addition, HMDD v2.0 presented more data that were generated based on concepts derived from the miRNA-disease association data, including disease spectrum width of miRNAs and miRNA spectrum width of human diseases. |
| Contain miRNA-disease association data from genetics, epigenetics, circulation samples and miRNA-target interactions |
| 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. User can search the database by miRNA and/or cancer names in the miRCancer Search page. Our website also provides two sequence analysis tools: clustering and chi-square analysis which can perform analysis on all or selected pool of miRNA sequences. |
| Search by miRNA or cancer name Containing sequence analysis based on cancer or species |
| StarBase v2.0 systematically identify the RNA–RNA and protein–RNA interaction networks. starBase 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 (HITS-CLIP, PAR-CLIP, iCLIP, CLASH) data and tumor samples (14 cancer types, >6000 samples). |
| Clinical and expression profiles of 14 cancer types (>6000 samples) Networks of CLIP-Seq experimentally supported miRNA-lncRNA and miRNA-mRNA interactions |
| Experimentally validated miRNA targets miRNA function |
| starBase v2.0 systematically identify the RNA–RNA and protein–RNA interaction networks. By combining 13 functional genomic annotations, we developed miRFunction and ceRNAFunction web servers to predict the function of miRNAs and other ncRNAs from the miRNA-mediated regulatory networks. |
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Predict the function of ncRNAs (miRNAs, lncRNAs, pseduogenes) |
| Experimentally validated miRNA targets miRNA roles in diseases |
| 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. |
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Including 8,000 cancer-related smRNA-seq datasets |
| miRNA expression |
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miTALOS v2 is a tool that provides insights into tissue specific miRNA regulation of biological pathways. miTALOS v2 developed a novel methodology for tissue specific pathway analysis of miRNAs. This database incorporated the most recent and highest quality miRNA targeting data (TargetScan and StarBase), RNA-seq based gene expression data (EBI Expression Atlas) and multiple new pathway data sources to increase the biological relevance of the predicted miRNA-pathway associations. |
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Including miRNA targeting data of TargetScan and StarBase, RNA-seq based gene expression data (EBI Expression Atlas) and multiple new pathway data sources |
| miRNA interactions in pathways |
| miR2GO web server is to provide a computational tool for the assessment of functional impacts of genetic and somatic mutations in miRNAs. The first function of this web server, miRmut2GO, allows users to analyze the changes of target genes caused by miRNA mutations and view the functional impacts of these changes in a gene ontology graph. This web server can also be used for analyzing the differences and similarities between the functions of different miRNAs. Different miRNAs perform different functions because they bind to different sets of target genes. The second function of the web server, miRpair2GO, allows users to perform comparative gene ontology analysis for the target gene sets of different miRNAs. |
| miRmut2GO assess the functional effects of mutations in miRNA seed regions miRpair2GO compares the functions of two miRNAs based on the enriched functional annotations of their target gene sets |
| CREAM (Chemotherapy ResistancE-Associated MiRSNP Database) is a database depositing the functional miRSNP associated with chemotherapy resistance. The term miRSNP was coined and defined as a novel class of functional single nucleotide polymorphisms (SNPs) that can interfere with microRNA (miRNA) function and result in loss of miRNA regulation of target gene. Various evidences have supported that miRSNPs play significant roles in regulating chemotherapy resistance. |
| Functional miRSNP associated with chemotherapy resistance |
| CHNmiRD is a web-based tool for inferring novel miRNA-disease associations based on a complex heterogeneous network (CHN) involving 402 miRNAs and 5080 diseases. CHNmiRD integrates multiple genomic and phenotype data, including protein-protein interaction data, gene ontology data, experimentally verified miRNA-target relationships, disease phenotype information and known miRNA-disease connections. |
| based on a complex heterogeneous network (CHN) involving 402 miRNAs and 5080 diseases |
| The Dietary microRNA Database is a searchable database of published and novel microRNA sequences discovered in human food. Each entry in the database represents the mature sequence of a food-born microRNA and may be retrieved along with its information about the genomic location and hairpin sequence of the parental pre-microRNA. 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. |
| Novel microRNA sequences discovered in human food |
| EpimiRBase is a manually curated database for researchers interested in the role of microRNAs in epilepsy. The fully searchable database includes information on up- and down-regulated microRNAs in the brain and blood, as well as functional studies, and covers both rodent models and human epilepsy. |
| Information on up and downregulated microRNAs in the brain and blood and functional studies Covers rodent models and human epilepsy |
| 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 |
| MicroSNiPer predicts the impact of a SNP on putative microRNA targets. This application interrogates the 3'-untranslated region and predicts if a SNP within the target site will disrupt/eliminate or enhance/create a microRNA binding site. MicroSNiPer computes these sites and examines the effects of SNPs in real time. |
| Search by gene or SNP |
| 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 |
| miRNA SNiPer is an online tool for the detection of miRNA polymorphisms in vertebrates and generated a catalog of miRNA seed region polymorphisms (miR-seed-SNPs) consisting of 149 SNPs in six species. Although a majority of detected polymorphisms were due to point mutations, two consecutive nucleotide substitutions were also identified in nine miRNAs. |
| Accepts a list of miRNA genes and returns a table of variations in pre-miRNA, mature, seed region |
| MirSNP is a collection of human SNPs in predicted miRNA-mRNA binding sites. We identified 414,510 SNPs that might affect miRNA-mRNA binding. Annotations were added to these SNPs to predict whether a SNP within the target site would decrease/break or enhance/create a miRNA-mRNA binding site |
| Search by gene, mRNA, miRNA or SNP |
| Mirsnpscore is a computational tool that can help identifying SNPs associated with diseases, by focusing on SNPs affecting miRNA-regulation of genes. The tool predicts the effects of SNPs in miRNA target sites and uses linkage disequilibrium to map these miRNA-related variants to SNPs of interest in GWAS. We compared our predicted SNP effects in miRNA target sites with measured SNP effects from allelic imbalance sequencing. Our predictions fit measured effects better than effects based on differences in free energy or differences of TargetScan context scores. |
| Search by gene, miRNA or SNP |
| multiMiR is a comprehensive collection of predicted and validated miRNA-target interactions and their associations with diseases and drugs. multiMiR collecting nearly 50 million records from 14 different databases. Expansion of databases based on disease annotation and drug response, in addition to many experimental and computational databases. |
| Using 11 predicted and validate miRNA-target Interactions Expansion of databases to those based on disease annotation and drug microRNA response |
| OncomiRDB database aiming 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. |
| miRNA regulates one cancer-related phenotype or cellular process miRNA directly regulates one oncogenic or tumor-suppressive gene |
| OncomiRdbB is a comprehensive database of oncomiRs mined from different existing databases for mouse and humans along with novel oncomiRs that we have validated in human breast cancer samples. The database also lists their respective predicted targets, identified using miRanda, along with their IDs, sequences, chromosome location and detailed description. This database facilitates querying by search strings including microRNA name, sequence, accession number, target genes and organisms. |
| Database of miRNAs, targets, their hubs and networks of various pathways which are involved in Breast cancer Targets involved in wnt, Jak- Stat, MAPK, mTOR, VEGF, Apoptosis and Notch pathways |
| The Patrocles database compiles DNA sequence polymorphisms (DSPs) that are predicted to perturb miRNA-mediated gene regulation. To support the biological relevance of Patrocles' content, we searched for signatures of selection acting on 'Patrocles single nucleotide polymorphisms (pSNPs)' in human and mice. As expected, we found a strong signature of purifying selection against not only SNPs that destroy conserved target sites but also against SNPs that create novel, illegitimate target sites, which is reminiscent of the Texel mutation in sheep |
| Polymorphic miRNA-mediated gene regulation Coverage of targets, miRNA precursors and silencing machinery |
| 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. |
| Assessment of miRNA based prognostic signatures for cancer clinical outcomes by multivariate survival analysis |
| 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 |
