ExpTreeDB: web-based query and visualization of manually annotated gene expression profiling experiments of human and mouse from GEO. Motivation: Numerous public microarray datasets are valuable resources for the scientific communities. Several online tools have made great steps to utilize 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 provides 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. Website is implemented in Perl, PHP, R, MySQL and Apache.

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  1. Mathé, Ewy (ed.); Davis, Sean (ed.): Statistical genomics. Methods and protocols (2016)