title: ExpTreeDB: web-based query and visualization of manually annotated gene expression profiling experiments of human and mouse from GEO.
abstract: BACKGROUND
  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.
  
  
  METHODS
  The database is freely available at http://biotech.bmi.ac.cn/ExpTreeDB. Web site is implemented in Perl, PHP, R, MySQL and Apache.
authors.affiliation: 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.
authors.forename: Ming
authors.initials: M
authors.lastname: Ni
authors.affiliation: 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.
authors.forename: Fuqiang
authors.initials: F
authors.lastname: Ye
authors.affiliation: 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.
authors.forename: Juanjuan
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authors.affiliation: 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.
authors.forename: Zongwei
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authors.lastname: Li
authors.affiliation: 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.
authors.forename: Shuai
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authors.lastname: Yang
authors.affiliation: 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.
authors.forename: Bite
authors.initials: B
authors.lastname: Yang
authors.affiliation: 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.
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authors.lastname: Han
authors.affiliation: 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.
authors.forename: Yongge
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authors.lastname: Wu
authors.affiliation: 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.
authors.forename: Ying
authors.initials: Y
authors.lastname: Chen
authors.affiliation: 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.
authors.forename: Fei
authors.initials: F
authors.lastname: Li
authors.affiliation: 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.
authors.forename: Shengqi
authors.initials: S
authors.lastname: Wang
authors.affiliation: 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.
authors.forename: Xiaochen
authors.initials: X
authors.lastname: Bo
mesh_terms: D000818:Animals; D015687:Cell Hypoxia / Q000235:genetics; D016000:Cluster Analysis; D030541:Databases, Genetic; D020869:Gene Expression Profiling / Q000379:methods*; D006801:Humans; D020407:Internet; D051379:Mice; D020411:Oligonucleotide Array Sequence Analysis; D012984:Software