RadAtlas 1.0: a knowledgebase focusing on radiation-associated genes

<b>Purpose:</b> 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. <b>Materials and methods:</b> 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. <b>Results:</b> 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. <b>Conclusions:</b> 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、电离水分子产生毒性自由基，还可诱发遗传效应与躯体效应。解析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，与辐射相关的基因功能信息隐匿于海量科学文献与各类数据库中，使得电离辐射响应机制的解析工作面临较大阻碍。**材料与方法：** 本研究通过文献与数据库挖掘的方式收集辐射相关基因，具体分别以PubMed收录的生物医学文献、GEO（Gene Expression Omnibus）的基因表达数据集为数据源开展挖掘工作。**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，该平台还提供了界面友好的Web交互界面，支持多种检索方式。**结论：** RadAtlas整合了大量与电离辐射相关的基因、生物学过程及通路信息，是首个同时收录带有文献佐证的辐射相关基因，以及带有差异表达佐证的潜在辐射相关基因的综合性目录资源。我们认为，RadAtlas将成为解析电离辐射响应机制的实用辅助工具。