PhenomiR. 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. Data was extracted from more than 365 scientific articles and resulted in more than 632 database entries as of 02 2011. The design principle of PhenomiR is to use established ontologies and resources. For annotation of diseases we use information of the OMIM Morbid Map, bioprocesses are described with terms from Gene Ontology and for annotation of tissue/cell culture information the Tissue Ontology is used. Publication: Ruepp A, Kowarsch A, Schmidl D, Buggenthin F, Brauner B, Dunger I, Fobo G, Frishman G, Montrone C, Theis FJ. The graph displays the connected part of the cancer network extracted from the PhenomiR database where only miRNAs with a minimal degree of 2 and a maximal degree of 5 were taken into consideration. DIANA LAB - mirExTra. FAME. Functional Assignment of MicroRNAs via Enrichment FAME is a software tool that uses computational target predictions in order to automatically infer the processes affected by human miRNAs.
The approach improves upon standard statistical tools by addressing specific characteristics of miRNA regulation. The analysis is based on a novel compendium of experimentally verified miRNA-pathway and miRNA-process associations that we constructed. FAME 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. An implementation of FAME that can be applied to gene expression data or any gene set is available as part of EXPANDER.
MiRSel: tab Search. MiRò.