REGene: A literature-based knowledgebase of animal regeneration that bridge tissue regeneration and cancer

Abstract

Regeneration is a common phenomenon across multiple animal phyla. Regeneration-related genes (REGs) are critical for fundamental cellular processes such as proliferation and differentiation. Identification of REGs and elucidating their functions may help to further develop effective treatment strategies in regenerative medicine. So far, REGs have been largely identified by small-scale experimental studies and a comprehensive characterization of the diverse biological processes regulated by REGs is lacking. Therefore, there is an ever-growing need to integrate REGs at the genomics, epigenetics, and transcriptome level to provide a reference list of REGs for regeneration and regenerative medicine research. Towards achieving this, we developed the first literature-based database called REGene (REgeneration Gene database). In the current release, REGene contains 948 human (929 protein-coding and 19 non-coding genes) and 8445 homologous genes curated from gene ontology and extensive literature examination. Additionally, the REGene database provides detailed annotations for each REG, including: gene expression, methylation sites, upstream transcription factors, and protein-protein interactions. An analysis of the collected REGs reveals strong links to a variety of cancers in terms of genetic mutation, protein domains, and cellular pathways. We have prepared a web interface to share these regeneration genes, supported by refined browsing and searching functions at http://REGene.bioinfo-minzhao.org/.