MirGeneDB

Welcome to MirGeneDB2.0 - the curated microRNA Gene Database

MirGeneDB is a database of microRNA genes that have been validated and annotated as described in "A Uniform System for the Annotation of Vertebrate microRNA Genes and the Evolution of the Human microRNAome".* The initial version contained 1,434 microRNA genes for human, mouse, chicken and zebrafish. Version 2.0 contains more than 7,500 genes from 32 organisms representing nearly every major metazoan group, and these microRNAs can be browsed, searched and downloaded.

New features to MirgeneDB2.0 include:

  1. Extensive expression data ranging from whole animal-samples to organs/tissues to cell-types based on publicly available datasets.
  2. Annotations of 3' non-templated uridylations, processing motifs, and of gene variants derived from alternative processing by Drosha and/or Dicer, are now provided for every miRNA.
  3. Updated annotations of the 3' ends for human, mouse, zebrafish and Daphnia based on publically available CAGE data.
  4. Comprehensive annotations of the evolutionary origin of both miRNA families (updated) and miRNA genes (new) with all orthologues and paralogues clearly identified both through name and through the heirarchy of the database. Further, the miRNA repertoires (both family and gene) are identified for all last common ancestors of the taxa included in the data base.
  5. All relevant fasta and annotation files (bed & gff) for all taxa are available for immediate download.
  6. All known false negatives are reported separately including the mature (and if known the star) read supporting the designation.

We are currently working on a manuscript for an official release later this month, but if you make use of the data presented here, please cite the Annual Reviews article in addition to the primary data sources.

Working title for MirGeneDB2.0 manuscript:

"MirGeneDB2.0: the curated microRNA Gene Database"

*Bastian Fromm1, Diana Domanska2, Michael Hackenberg3, Anthony Mathelier4,5, Eirik Høye1, Morten Johansen6, Eivind Hovig1,2,6, Kjersti Flatmark1,7,8 & Kevin J. Peterson9

1Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Nydalen, N-0424 Oslo, Norway

2Department of Informatics, University of Oslo, Blindern, N-0318 Oslo, Norway

3Department of Genetics, Faculty of Sciences, University of Granada, Granada, 1s8071, Spain

4Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, N-0318 Oslo, Norway

5Department of Cancer Genetics, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital Radiumhospitalet, N-0424 Oslo, Norway

6Institute for Medical Informatics,The Norwegian Radium Hospital, Oslo University Hospital, N-0424 Oslo, Norway

7Department of Gastroenterological Surgery, The Norwegian Radium Hospital, Oslo University Hospital, Nydalen, N-0424 Oslo, Norway

8Institute of Clinical Medicine, University of Oslo, Blindern, N-0318 Oslo, Norway

9Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire 03755, U.S.