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circMine: a comprehensive database to integrate, analyze and visualize human disease-related circRNA transcriptome

文献类型：期刊论文

作者Zhang, Wenliang1,2,9; Liu, Yang2,3,10; Min, Zhuochao4; Liang, Guodong12; Mo, Jing9; Ju, Zhen2,6,7; Zeng, Binghui8,9; Guan, Wen9,11; Zhang, Yan2; Chen, Jianliang1
刊名NUCLEIC ACIDS RESEARCH
出版日期2022-01-07
卷号50期号:D1页码:D83-D92
ISSN号0305-1048
DOI10.1093/nar/gkab809
英文摘要Many circRNA transcriptome data were deposited in public resources, but these data show great heterogeneity. Researchers without bioinformatics skills have difficulty in investigating these invaluable data or their own data. Here, we specifically designed circMine (http://hpcc.siat.ac.cn/circmine and 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 13 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 13 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. In summary, circMine provides user-friendly web interfaces to browse, search, analyze and download data freely, and submit new data for further integration, and it can be an important resource to discover significant circRNA in different diseases.
资助项目National Key R&D Program of China[2018YFB0204403] ; Guangdong Basic and Applied Basic Research Foundation, China[2020A1515110528] ; National Natural Science Foundation of China[32100513] ; China Postdoctoral Science Foundation[2021M693302] ; Strategic Priority CAS Project[XDB38000000] ; Shenzhen Basic Research Fund[RCYX2020071411473419] ; Shenzhen Basic Research Fund[KQTD20200820113106007] ; Shenzhen Basic Research Fund[JSGG20201102163800001] ; Sanming Project of Medicine (Shenzhen)[SZSM201911016]
WOS研究方向Biochemistry & Molecular Biology
语种英语
WOS记录号WOS:000743496700010
出版者OXFORD UNIV PRESS
源URL[http://119.78.100.204/handle/2XEOYT63/18237]  
专题中国科学院计算技术研究所期刊论文_英文
通讯作者Zhang, Wenliang; Wei, Yanjie; Chan, Godfrey Chi-Fung
作者单位1.Univ Hong Kong, Dept Pediat, Shenzhen Hosp, Shenzhen 518053, Guangdong, Peoples R China
2.Chinese Acad Sci Shenzhen, Shenzhen Inst Adv Technol, Shenzhen 518055, Guangdong, Peoples R China
3.Univ Hong Kong, Dept Gastroenterol & Hepatol, Shenzhen Hosp, Shenzhen 518053, Guangdong, Peoples R China
4.Univ Elect Sci & Technol China, Sch Informat & Software Engn, Chengdu 610054, Peoples R China
5.Univ Hong Kong, Dept Pediat & Adolescent Med, LKS Fac Med, 21 Sassoon Rd, Hong Kong 999077, Peoples R China
6.Chinese Acad Sci, Shenzhen Inst Adv Technol, Ctr High Performance Comp, Shenzhen 518055, Guangdong, Peoples R China
7.Chinese Acad Sci, Shenzhen Inst Adv Technol, CAS Key Lab Hlth Informat, Shenzhen 518055, Guangdong, Peoples R China
8.Sun Yat Sen Univ, Hosp Stomatol, Guangdong Prov Key Lab Stomatol, Guanghua Sch Stomatol, Guangzhou 510055, Peoples R China
9.Outstanding Biotechnol Co Ltd Shenzhen, Dept Bioinformat, Shenzhen 518053, Peoples R China
10.Jilin Business & Technol, Expt Training Management Ctr, Changchun 130507, Jilin, Peoples R China
推荐引用方式
GB/T 7714		 Zhang, Wenliang,Liu, Yang,Min, Zhuochao,et al. circMine: a comprehensive database to integrate, analyze and visualize human disease-related circRNA transcriptome[J]. NUCLEIC ACIDS RESEARCH,2022,50(D1):D83-D92.
APA Zhang, Wenliang.,Liu, Yang.,Min, Zhuochao.,Liang, Guodong.,Mo, Jing.,...&Chan, Godfrey Chi-Fung.(2022).circMine: a comprehensive database to integrate, analyze and visualize human disease-related circRNA transcriptome.NUCLEIC ACIDS RESEARCH,50(D1),D83-D92.
MLA Zhang, Wenliang,et al."circMine: a comprehensive database to integrate, analyze and visualize human disease-related circRNA transcriptome".NUCLEIC ACIDS RESEARCH 50.D1(2022):D83-D92.

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来源：计算技术研究所

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