Publications that have contributed to EpimiRBase to date can be found on our publications page.
Below are other databases and tools related to EpimiRBase.
miRNAmeConverter (to be published in 2016)
MicroRNA names from each publication were mapped to miRBase 21 using the R package miRNAmeConverter. MicroRNAs that could not be unambiguously mapped to miRBase 21, or that were not included in miRBase 21 were removed. miRNAmeConverter has been submitted to Bioconductor for review and a manuscript describing the package is in preparation. Please contact Stefan Haunsberger for details at:
miRBase: the microRNA database
miRBase is a searchable database of published miRNA sequences and annotation. Each entry in the miRBase Sequence database represents a predicted hairpin portion of a miRNA transcript, with information on the location and sequence of the mature miRNA sequence. Both hairpin and mature sequences are available for searching and browsing, and entries can also be retrieved by name, keyword, references and annotation. All sequence and annotation data are also available for download.
There has been concern that many of the sequences in miRBase are not derived from bona fide microRNA genes. MirGeneDB is a recently published database of manually curated and highly supported bona fide microRNAs (Fromm et al., 2015). For example, of the 1,881 human microRNAs listed in miRBase, only 523 meet the standards for microRNA annotation in MirGeneDB.
miRTarBase: the experimentally validated microRNA-target interactions database
miRTarBase has accumulated more than three hundred and sixty thousand miRNA-target interactions (MTIs), which are collected by manually surveying pertinent literature after NLP of the text systematically to filter research articles related to functional studies of miRNAs. Generally, the collected MTIs are validated experimentally by reporter assay, western blot, microarray and next-generation sequencing experiments.
DIANA-TarBase v7.0, provides more than half a million high quality manually curated experimentally validated miRNA:gene interactions in 356 different cell types from 24 species, enhanced with detailed meta-data including positive or negative experimental results, the utilised experimental methodology, experimental conditions including cell/tissue type and treatment.