Ming Ni1, Fuqiang Ye1, Juanjuan Zhu2, Zongwei Li1, Shuai Yang1, Bite Yang1, Lu Han1, Yongge Wu1, Ying Chen1, Fei Li1, Shengqi Wang2, Xiaochen Bo1. 1. Beijing Institute of Radiation Medicine, Beijing 100850, College of Life Sciences, Jilin University, Changchun 130012 and Henan University of Traditional Chinese Medicine, Zhengzhou 450008, China. 2. Beijing Institute of Radiation Medicine, Beijing 100850, College of Life Sciences, Jilin University, Changchun 130012 and Henan University of Traditional Chinese Medicine, Zhengzhou 450008, China Beijing Institute of Radiation Medicine, Beijing 100850, College of Life Sciences, Jilin University, Changchun 130012 and Henan University of Traditional Chinese Medicine, Zhengzhou 450008, China.
Abstract
MOTIVATION: Numerous public microarray datasets are valuable resources for the scientific communities. Several online tools have made great steps to use these data by querying related datasets with users' own gene signatures or expression profiles. However, dataset annotation and result exhibition still need to be improved. RESULTS: ExpTreeDB is a database that allows for queries on human and mouse microarray experiments from Gene Expression Omnibus with gene signatures or profiles. Compared with similar applications, ExpTreeDB pays more attention to dataset annotations and result visualization. We introduced a multiple-level annotation system to depict and organize original experiments. For example, a tamoxifen-treated cell line experiment is hierarchically annotated as 'agent→drug→estrogen receptor antagonist→tamoxifen'. Consequently, retrieved results are exhibited by an interactive tree-structured graphics, which provide an overview for related experiments and might enlighten users on key items of interest. AVAILABILITY AND IMPLEMENTATION: The database is freely available at http://biotech.bmi.ac.cn/ExpTreeDB. Web site is implemented in Perl, PHP, R, MySQL and Apache.
MOTIVATION: Numerous public microarray datasets are valuable resources for the scientific communities. Several online tools have made great steps to use these data by querying related datasets with users' own gene signatures or expression profiles. However, dataset annotation and result exhibition still need to be improved. RESULTS: ExpTreeDB is a database that allows for queries on human and mouse microarray experiments from Gene Expression Omnibus with gene signatures or profiles. Compared with similar applications, ExpTreeDB pays more attention to dataset annotations and result visualization. We introduced a multiple-level annotation system to depict and organize original experiments. For example, a tamoxifen-treated cell line experiment is hierarchically annotated as 'agent→drug→estrogen receptor antagonist→tamoxifen'. Consequently, retrieved results are exhibited by an interactive tree-structured graphics, which provide an overview for related experiments and might enlighten users on key items of interest. AVAILABILITY AND IMPLEMENTATION: The database is freely available at http://biotech.bmi.ac.cn/ExpTreeDB. Web site is implemented in Perl, PHP, R, MySQL and Apache.
Authors: Yin Ni; Caiyun Song; Shuqing Jin; Zhoufeng Chen; Ming Ni; Lu Han; Jiansheng Wu; Yin Jin Journal: J Int Med Res Date: 2017-04-24 Impact factor: 1.671