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Comparative Models of Regeneration Database (RegenDB)
Michael C. Rosenstein1, Viravuth P. Yin1 and Benjamin L. King1
1
MDI Biological Laboratory, Salisbury Cove, Maine 04672
[email protected]
The Comparative Models of Regeneration Database (RegenDB) provides a
systems-level view of tissue regeneration models to advance knowledge of regenerative
biology and stem cell self-renewal. Scientists can use RegenDB to analyze integrated
functional genomic datasets of regenerative processes to identify conserved gene
networks within and across species. RegenDB represents genes and transcripts, homology
relationships, gene expression data, microRNA target predictions, gene interactions,
pathways, and Gene Ontology annotations, all in multiple organisms. Expression data
are re-analyzed regularly to use current annotation and consistent analysis methods.
Homology relationships can be used to find genes consistently differentially expressed
during regeneration across organisms. For example, a comparison of zebrafish and
neonatal mouse heart regeneration showed 336 common orthologs were differentially
expressed, including the macrophage scavenger receptor, marco. Significantly, new
hypotheses about the regulation of differentially expressed genes by microRNAs may be
made using RegenDB. For example, users may investigate how groups of microRNAs
(e.g., miR-21, miR-31 and miR-181) regulate genes that are differentially expressed
during zebrafish heart regeneration and that belong to a particular pathway (e.g., gap
junction assembly) or have a particular function (e.g., heart development). RegenDB
consists of a relational database with load and web interface software built on a robust
architecture. We continue to enhance RegenDB by adding new functionality and
datasets.