title: OGEE v2: an update of the online gene essentiality database with special focus on differentially essential genes in human cancer cell lines.
abstract: OGEE is an Online GEne Essentiality database. To enhance our understanding of the essentiality of genes, in OGEE we collected experimentally tested essential and non-essential genes, as well as associated gene properties known to contribute to gene essentiality. We focus on large-scale experiments, and complement our data with text-mining results. We organized tested genes into data sets according to their sources, and tagged those with variable essentiality statuses across data sets as conditionally essential genes, intending to highlight the complex interplay between gene functions and environments/experimental perturbations. Developments since the last public release include increased numbers of species and gene essentiality data sets, inclusion of non-coding essential sequences and genes with intermediate essentiality statuses. In addition, we included 16 essentiality data sets from cancer cell lines, corresponding to 9 human cancers; with OGEE, users can easily explore the shared and differentially essential genes within and between cancer types. These genes, especially those derived from cell lines that are similar to tumor samples, could reveal the oncogenic drivers, paralogous gene expression pattern and chromosomal structure of the corresponding cancer types, and can be further screened to identify targets for cancer therapy and/or new drug development. OGEE is freely available at http://ogee.medgenius.info.
authors: Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology (HUST), 430074 Wuhan, Hubei, China weihuachen@hust.edu.cn.
authors: Wei-Hua
authors: WH
authors: Chen
authors: Department of Blood Transfusion, Tangdu Hospital, the Fourth Military Medical University, No 1, Xinsi Road, Chanba District, 710000 Xi'an, China.
authors: Guanting
authors: G
authors: Lu
authors: Department of Computer Science and Technology, Tongji University, Shanghai 201804, China.
authors: Xiao
authors: X
authors: Chen
authors: Department of Computer Science and Technology, Tongji University, Shanghai 201804, China.
authors: Xing-Ming
authors: XM
authors: Zhao
authors: European molecular biology laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany.|Molecular Medicine Partnership Unit, University of Heidelberg and European Molecular Biology Laboratory, 69120 Heidelberg, Germany.|Max-Delbrück-Centre for Molecular Medicine, Robert-Rössle-Straße 10, 13125 Berlin, Germany.|Department of Bioinformatics, Biocenter, University of Würzburg, 97074 Würzburg, Germany.
authors: Peer
authors: P
authors: Bork
mesh_terms: D045744:Cell Line, Tumor; D030561:Databases, Nucleic Acid; D015972:Gene Expression Regulation, Neoplastic; D020043:Genes, Essential; D006801:Humans; D009369:Neoplasms / Q000235:genetics*; D009857:Oncogenes; D057386:Search Engine; D012984:Software; D014584:User-Computer Interface; D064878:Web Browser