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RadAtlas 1.0: a knowledgebase focusing on radiation-associated genes.
International Journal of Radiation Biology ( IF 2.6 ) Pub Date : 2020-05-12 , DOI: 10.1080/09553002.2020.1761567
Hao Xu 1 , Yuan Liu 1 , Yang Li 1 , Lihong Diao 1 , Ziyu Xun 1 , Yuqi Zhang 1 , Zhidong Wang 2 , Dong Li 1
Affiliation  

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.



中文翻译:

RadAtlas 1.0:一个专注于辐射相关基因的知识库。

目的:电离辐射具有非常复杂的生物学效应,例如引起对DNA和蛋白质的破坏,使水分子离子化以产生有毒的自由基以及引发遗传和体细胞效应。了解放射线的生物分子反应机制对于预防和治疗放射线疾病非常重要。然而,这些与辐射有关的基因的功能信息被许多科学论文和数据库所掩盖,从而使人们难以理解电离辐射的响应机制。

材料和方法:我们通过文献和数据库挖掘收集了与辐射相关的基因。文献和数据库挖掘分别基于PubMed的生物医学文献和GEO的基因表达数据集进行。

结果:我们建立了一个与电离辐射相关的知识库RadAtlas 1.0(http://biokb.ncpsb.org/radatlas),其中包含从文献挖掘中汇编的598个与辐射相关的基因,以及从美国基因表达数据集中收集的611个与辐射相关的潜在基因。差异基因表达分析。我们还提供了一个用户友好的Web界面,其中提供了多种搜索方法。

结论: RadAtlas收集了大量有关基因,生物学过程以及与电离辐射有关的途径的信息。这是首次尝试提供具有文学证据的辐射相关基因和具有差异表达证据的潜在辐射相关基因的完整目录。我们相信RadAtlas将是了解电离辐射响应机制的有用工具。

更新日期:2020-05-12
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