circMine

NAR Molecular Biology Database Collection entry number 2306

http://www.biomedical-web.com/circmine

Zhang, Wenliang; Liu, Yang; Min, Zhuochao; Liang, Guodong; Mo, Jing; Ju, Zhen; Zeng, Binghui,; Guan, Wen; Zhang, Yan; Chen, Jianliang; Zhang, Qianshen; Li, Hanguang; Zeng, Chunxia; Wei, Yanjie; Chan, Godfrey Chi Fung

Department of Pediatrics, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong, 518053, China
Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong, 518055, China; Department of Gastroenterology and Hepatology, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong, 518053, China;
School of Information and Software Engineering, University of Electronic Science and Technology of China, Chengdu, 610054, China;
Department of Pediatrics and Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, 21 Sassoon Road, Hong Kong; Center for High Performance Computing, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong, 518055, China;
CAS Key Laboratory of Health Informatics, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong, 518055, China;
Hospital of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou, 510055, China;
Department of Bioinformatics, Outstanding Biotechnology Co., Ltd. Shenzhen, Shenzhen, China; Experimental Training Management Center, Jilin Business and Technology, Jilin Province, 130507, China;
Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, 510260, China;
Department of Colorectal and Stomach Cancer Surgery, Jilin Cancer Hospital, Changchun, Jilin, 130000, China.

Contact zhangwl25@mail3.sysu.edu.cn; yj.wei@siat.ac.cn ;  gcfchan@hku.hk

Many circRNA transcriptome data were deposited in public resources, but these data show great heterogeneity. Researchers without bioinformatics skills have difficulty in investigating these nvaluable data or their own data. To overcome the above challenges, we specifically designed circMine ( http://hpcc.siat.ac.cn/circmine & http://www.biomedical-web.com/circmine/ ) that provides 1,821,448 entries formed by 136,871 circRNAs, 87 diseases, and 120 circRNA transcriptome datasets of 1107 samples across 31 human body sites. circMine further provides thirteen online analytical functions to comprehensively investigate these datasets to evaluate the clinical and biological significance of circRNA. To improve the data applicability, each dataset was standardized and annotated with relevant clinical information. All of the thirteen analytic functions allow users to group samples based on their clinical data and assign different parameters for different analyses, and enable them to perform these analyses using their own circRNA transcriptomes. Moreover, three additional tools were developed in circMine to systematically discover the circRNA-miRNA interaction and circRNA translatability. For example, we systematically discovered five potential translatable circRNAs associated with prostate cancer progression using circMine. Furthermore, comparative results suggested that circMine is significantly different from all the existing circRNA databases and tools, and it provides a new data and function platform that is not currently available. In summary, circMine provides user-friendly web interfaces to browse, search, analyze, download data freely, and submit new data for further integration, and it can be an important resource to discover significant circRNA in different diseases.

We thank the supports from The Clinical, Translational and Basic Research Laboratory of The University of Hong Kong - Shenzhen Hospital.

Go to the article in the NAR Database issue.

https://doi.org/10.1093/nar/gkab809

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