RegenDbase: a comparative database of noncoding RNA regulation of tissue regeneration circuits across multiple taxa

RegenDbase provides fundamental analyses of regeneration circuits within individual experiments and comparative analyses across experiments and species. a Organizational workflow for multi-layered data processing and analysis of published (public) and unpublished (internal) gene expression datasets. b Examples of how RegenDbase was used to compare: (i) genes common or unique to two pairwise contrasts of early stages of zebrafish heart regeneration (0 vs. 1？dpa and 0 vs. 3？dpa); (ii) genes common or unique to contrasts from early stages of zebrafish caudal fin regeneration (0 vs. 4？dpa) and zebrafish heart regeneration (0 vs. 3？dpa); (iii) comparative analyses of early zebrafish heart (0 vs. 3？dpa) and neonatal mouse heart (0 vs. 1？dpa) regeneration showing the number of orthologs commonly differentially expressed along with the number of zebrafish and mouse genes unique to each model. c Heatmap representing genes from precomputed pairwise contrasts from a subset of significantly up- and downregulated transcripts between uninjured and 3 days post-amputation (dpa) regenerating adult ventricles. The temporal expression profile for cxcr4b, an essential regeneration gene, is shown as a boxplot in the web interfac