Tutorials and FAQs of miRSponge
- Overview of miRSponge
- Search
- Browse
- miRSponge data table
- miRSponge details
- Functional Annotation of miRSponges
- Overview of miRSponge
- Dysregulated expression of miRNAs can result disrupt proliferation, differentiation and apoptosis. Emerging evidence suggests that miRNAs are themselves regulated by endogenous molecules containing miRNA binding sites, such as pseudogenes, long noncoding RNAs, and circular RNAs. Termed 'miRNA sponges', these competitive inhibitors competitively sequester miRNAs, preventing them from interacting with their natural targets. The endogenous miRNA sponges and targets or competing endogenous RNAs (ceRNAs) act dynamically to balance the expression of each other. This balance is important for various physiological processes, and disruption can result in pathological states.
- Statistics: The experimentally validated miRSponge database (miRSponge) recorded 576 sponge-miRNA interactions and 457 ceRNA associations in 11 species, following manual curating from nearly 1000 articles. Class of sponges include endogenously generated molecules such as coding-genes, pseudogenes, long noncoding RNAs and circular RNAs, and exogenously introduced molecules such as viral RNAs and artificial engineered sponges.
- Around 70% of the interactions were experimentally identified in diseased states. Each entry contains detailed information on sponges, miRNAs and competing targets, species, miRBase accession, HGNC and GeneCards annotation, tissue distribution, conditions for detection, corresponding literature, PMIDs, a brief description of the sponge-miRNA interaction, and the experimental method used to characterize the association. miRSponge provides a user-friendly interface for convenient browsing, retrieval and downloading. In addition, miRSponge offers a submission page for newly validated miRNA-sponge and ceRNA association data.
- In summary, the miRSponge database could significantly improve our understanding of transcriptome communication among different RNA classes, and provides a timely and valuable resource for miRNA research and clinical applications.
- Search
- Browse
- miRSponge data table
- miRSponge details
- Functional Annotation of miRSponges
miRSponge provided users a quick search facilitate data extraction and download in a flexible way. Quick search allows users to input names of sponges / microRNA / Gene / species / disease. miRSponge will automatically recognize the input type.
Browse page allows users to browse the miRSponge database. By clicking the "file tree" on the left, corresponding dataset will be listed on the right. Currently, the "file tree" contains three branches (miRNAs, sponges, species).
miRSponge results are organized in a table. Each line represents one miRSponge record, including miRNA and gene information. Each miRSponge record contains the sponge type, sponge name, miRNA, gene, species, PubMed ID and further detailed information. Users can download the entire data table by clicking the download button, and can view the more detailed information by clicking the detail button.
To maximize information content, a variety of biological annotations were integrated. Each entry includes detailed information on sponges, miRNAs and competing targets, species, miRBase accession, HGNC and GeneCard annotation, tissue distribution, conditions for detection, associated diseases, corresponding literature, PMIDs and a brief description of the competitive interaction and experimental method used for characterization. miRNA binding sites including sequence alignment score and thermodynamic free energy (predicted by miRanda) on the sponge were provided. Predicted information of miRNA-sponge or ceRNA ineractions, which related with starBaseV2.0 and DIANA-LncBase, has also been provided.
miRSponge is also a comprehensive miRNA Sponges / ceRNAs functional annotations sever.Given that some miRNA sponges such as lncRNAs are still poorly understood, functional annotation (Gene Ontology and canonical pathways such as BioCarta, KEGG, Reactome etc.) including the natural miRNA targets and experimentally validated database entries (TarBase6.0 , miRecord (23), miR2Disease and miRTarBase) were included for each sponge. A guilty-by-association strategy has been used previously to analyze lncRNA function , and miRSponge provides significantly enriched GO terms and pathways for each miRNA sponge (Hypergeometric test, P<0.01). By implementing the DAVID API tool , miRSponge allows users to perform multi-context functional analyses.
