RadAtlas 1.0: a knowledgebase focusing on radiation-associated genes

Purpose: Ionizing radiation has very complex biological effects, such as inducing damage to DNA and proteins, ionizing water molecules to produce toxic free radicals, and triggering genetic and somatic effects. Understanding the biomolecular response mechanism of radiation is very important for the prevention and treatment of radiation diseases. However, function information of these radiation-associated genes is hidden in numbers of scientific papers and databases, making it difficult to understand the response mechanism of ionizing radiation. Materials and methods: We collected radiation-associated genes by literature and database mining. Literature and database mining was performed on the basis of biomedical literature from PubMed and gene expression datasets from GEO respectively. Results: We built an ionizing radiation related knowledgebase RadAtlas 1.0 (http://biokb.ncpsb.org/radatlas), which contains 598 radiation-associated genes compiled from literature mining, and 611 potential radiation-associated genes collected from gene expression datasets by differential gene expression analysis. We also provide a user-friendly web interface that offers multiple search methods. Conclusions: RadAtlas collected a large amount of information about genes, biological processes, and pathways related to ionizing radiation. It is the first attempt to provide a comprehensive catalog of radiation-associated genes with literature evidence and potential radiation-associated genes with differential expression evidence. We believe that RadAtlas would be a helpful tool to understand the response mechanism to ionizing radiation.研究目的：电离辐射具有极为复杂的生物学效应，可诱导DNA与蛋白质损伤、使水分子电离产生毒性自由基，并引发遗传效应与躯体效应。阐明辐射的生物分子响应机制，对于辐射疾病的预防与治疗具有重要意义。然而，辐射相关基因的功能信息隐匿于海量科研论文与数据库中，极大阻碍了人们对电离辐射响应机制的深入理解。 材料与方法：本研究通过文献与数据库挖掘手段收集辐射相关基因。具体分别基于PubMed收录的生物医学文献与GEO基因表达数据集开展文献与数据库挖掘工作。 研究结果：本研究构建了电离辐射相关知识库RadAtlas 1.0（网址：http://biokb.ncpsb.org/radatlas），该知识库包含通过文献挖掘得到的598个辐射相关基因，以及通过差异基因表达分析从基因表达数据集中筛选得到的611个潜在辐射相关基因。此外，该平台还提供了操作友好的网页交互界面，支持多种检索方式。 结论：RadAtlas收录了大量与电离辐射相关的基因、生物学过程及信号通路信息。本研究首次尝试构建涵盖经文献证实的辐射相关基因与经差异表达验证的潜在辐射相关基因的综合目录。我们认为，RadAtlas将成为阐明电离辐射响应机制的有力辅助工具。