OUGENE： a disease associated over-expressed and under-expressed gene database

• Published in: Science bulletin (Beijing) 2016-05, Vol.61 (10), p.752-754
• Main Authors: Pan, Xiaoyong, Shen, Hong-Bin
• Format: Article
• Language: English
• Subjects: Chemistry/Food Science; Disease; Earth Sciences; Engineering; Gene over- and under-expression; Humanities and Social Sciences; Letter; Life Sciences; multidisciplinary; Physics; Science; Science (multidisciplinary); Text mining; Web界面; 专业数据库; 人类疾病; 基因数据库; 表型变异; 过度表达; 过表达; 金
• ISSN: 2095-9273; 2095-9281
• DOI: 10.1007/s11434-016-1059-1

Gene over-expression or under-expression is closely associated with human diseases, which contributes to phenotypic variations and diversity. To our best knowledge, there is no single open specific resource available to provide the association information between gene over- or under-expression and various diseases. In this study, we presented a comprehensive disease-associated over- and under-expressed gene database （OUGene） based on our proposed text mining pipeline and several open curated databases. It contains total 41,269 unique associa- tions between 7,238 over- or under-expressed genes and 1,480 diseases, which are supported by 81,974 evidence sentences from 56,442 articles. The OUGene is compre- hensive and covers most important therapeutic areas. Meanwhile a new scoring system is designed to rank the associations based on benchmarking against hand-curated data. OUGene provides an easy-of-use web interface for researchers to analyze these data and visualize the associ- ated networks, which can give insights to the complex relationships between over- and under-expressed genes and diseases at a system level. It is available at www.csbio.sjtu. edu.cn/bioinf/OUGene/.