| 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 |
| 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 |
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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 |
