Dataset Information

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/.

SUBMITTER: Zhao M

PROVIDER: S-EPMC4791596 | biostudies-literature | 2016 Mar

REPOSITORIES: biostudies-literature

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

Zhao Min M Rotgans Bronwyn B Wang Tianfang T Cummins S F SF

Scientific reports 20160315

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 ...[more]

PMID: 26975833

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Project description:The peripheral nervous system has an astonishing ability to regenerate following a compression or crush injury; however, the potential for full repair following a transection injury is much less. Currently, the major clinical challenge for peripheral nerve repair come from long gaps between the proximal and distal nerve stumps, which prevent regenerating axons reaching the distal nerve. Precise axon targeting during nervous system development is controlled by families of axon guidance molecules including Netrins, Slits, Ephrins and Semaphorins. Several recent studies have indicated key roles of Netrin1, Slit3 and EphrinB2 signalling in controlling the formation of new nerve bridge tissue and precise axon regeneration after peripheral nerve transection injury. Inside the nerve bridge, nerve fibroblasts express EphrinB2 while migrating Schwann cells express the receptor EphB2. EphrinB2/EphB2 signalling between nerve fibroblasts and migrating Schwann cells is required for Sox2 upregulation in Schwann cells and the formation of Schwann cell cords within the nerve bridge to allow directional axon growth to the distal nerve stump. Macrophages in the outermost layer of the nerve bridge express Slit3 while migrating Schwann cells and regenerating axons express the receptor Robo1; within Schwann cells, Robo1 expression is also Sox2-dependent. Slit3/Robo1 signalling is required to keep migrating Schwann cells and regenerating axons inside the nerve bridge. In addition to the Slit3/Robo1 signalling system, migrating Schwann cells also express Netrin1 and regenerating axons express the DCC receptor. It appears that migrating Schwann cells could also use Netrin1 as a guidance cue to direct regenerating axons across the peripheral nerve gap. Engineered neural tissues have been suggested as promising alternatives for the repair of large peripheral nerve gaps. Therefore, understanding the function of classic axon guidance molecules in nerve bridge formation and their roles in axon regeneration could be highly beneficial in developing engineered neural tissue for more effective peripheral nerve repair.

Project description:Background: The approach to farm animal welfare evaluation has changed and animal-based measures (ABM), defined as the responses of an animal or effects on an animal, were introduced to assess animal welfare. Animal-based measures can be taken directly on the animal or indirectly and include the use of animal records. They can result from a specific event or be the cumulative outcome of many days, weeks, or months. The objective of the current study was to analyze the use of general ABM codified terms in the scientific literature, the presence of their definitions, and the gap mapping of their use across animal species, categories, years of publication, and geographical areas of the corresponding author's institution. The ultimate aim was to propose a common standard terminology to improve communication among stakeholders. In this study, data models were populated by collecting information coming from scientific papers extracted through a transparent and reproducible protocol using Web of ScienceTM and filtering for the general ABM codified terms (or synonyms/equivalents). A total of 199 papers were retained, and their full texts were assessed. The frequency of general codified ABM terms was analyzed according to the classification factors listed in the objectives. These papers were prevalently European (159 documents), and the most represented species was cattle. Fifty percent of the papers did not provide a definition of the general ABM terms, and 54% cited other sources as reference for their definition. The results of the study showed a very low penetration of the general codified ABM term in the literature on farm animal welfare, with only 1.5% of the papers including the term ABM. This does not mean that specific ABM are not studied, but rather that these specific ABM are not defined as such under a common umbrella, and there is no consensus on the use of terminology, not even among scientists. Thus, we cannot expect the stakeholders to use a common language and a standardized terminology. The recognition and the inclusion of ABM in the lists of commonly accepted abbreviations of scientific journals could be a first step to harmonize the terminology in the scientific literature.

Dataset Information

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

Publications

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

Similar Datasets

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