MNDR v3.0: mammal ncRNA-disease repository with increased coverage and annotation

被引:104
作者
Ning, Lin [1 ]
Cui, Tianyu [2 ]
Zheng, Boyang [2 ]
Wang, Nuo [2 ]
Luo, Jiaxin [2 ]
Yang, Beilei [2 ]
Du, Mengze [3 ]
Cheng, Jun [4 ]
Dou, Yiying [2 ]
Wang, Dong [1 ,2 ,5 ]
机构
[1] Southern Med Univ, Dermatol Hosp, Guangzhou 510091, Peoples R China
[2] Southern Med Univ, Sch Basic Med Sci, Dept Bioinformat, Guangzhou 510515, Peoples R China
[3] Guangzhou Med Univ, Affiliated Hosp 6, Qingyuan Peoples Hosp, B24 Yinquan South Rd, Qingyuan 511518, Guangdong, Peoples R China
[4] Southern Med Univ, Affiliated Foshan Matern & Child Healthcare Hosp, Foshan Matern & Child Healthcare Hosp, Guangzhou, Peoples R China
[5] Univ Elect Sci & Technol China, Ctr Informat Biol, Chengdu 611731, Peoples R China
基金
中国国家自然科学基金;
关键词
LONG NONCODING RNAS; DATABASE; ASSOCIATIONS; RESOURCE;
D O I
10.1093/nar/gkaa707
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
Many studies have indicated that non-coding RNA (ncRNA) dysfunction is closely related to numerous diseases. Recently, accumulated ncRNA-disease associations have made related databases insufficient to meet the demands of biomedical research. The constant updating of ncRNA-disease resources has become essential. Here, we have updated the mammal ncRNA-disease repository (MNDR, http:// www.rna-society.org/mndr/) to version 3.0, containing more than one million entries, four-fold increment in data compared to the previous version. Experimental and predicted circRNA-disease associations have been integrated, increasing the number of categories of ncRNAs to five, and the number of mammalian species to 11. Moreover, ncRNA-disease related drug annotations and associations, as well as ncRNA subcellular localizations and interactions, were added. In addition, three ncRNA-disease (miRNA/lncRNA/circRNA) prediction tools were provided, and the website was also optimized, making it more practical and user-friendly. In summary, MNDR v3.0 will be a valuable resource for the investigation of disease mechanisms and clinical treatment strategies.
引用
收藏
页码:D160 / D164
页数:5
相关论文
共 57 条
[1]   LncRNADisease 2.0: an updated database of long non-coding RNA-associated diseases [J].
Bao, Zhenyu ;
Yang, Zhen ;
Huang, Zhou ;
Zhou, Yiran ;
Cui, Qinghua ;
Dong, Dong .
NUCLEIC ACIDS RESEARCH, 2019, 47 (D1) :D1034-D1037
[2]   MDHGI: Matrix Decomposition and Heterogeneous Graph Inference for miRNA-disease association prediction [J].
Chen, Xing ;
Yin, Jun ;
Qu, Jia ;
Huang, Li .
PLOS COMPUTATIONAL BIOLOGY, 2018, 14 (08)
[3]   NRDTD: a database for clinically or experimentally supported non-coding RNAs and drug targets associations [J].
Chen, Xing ;
Sun, Ya-Zhou ;
Zhang, De-Hong ;
Li, Jian-Qiang ;
Yan, Gui-Ying ;
An, Ji-Yong ;
You, Zhu-Hong .
DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION, 2017,
[4]   Constructing lncRNA functional similarity network based on lncRNA-disease associations and disease semantic similarity [J].
Chen, Xing ;
Yan, Chenggang Clarence ;
Luo, Cai ;
Ji, Wen ;
Zhang, Yongdong ;
Dai, Qionghai .
SCIENTIFIC REPORTS, 2015, 5
[5]   Circular RNAs in immune responses and immune diseases [J].
Chen, Xu ;
Yang, Tian ;
Wang, Wei ;
Xi, Wenjin ;
Zhang, Tianze ;
Li, Qi ;
Yang, Angang ;
Wang, Tao .
THERANOSTICS, 2019, 9 (02) :588-607
[6]   DincRNA: a comprehensive web-based bioinformatics toolkit for exploring disease associations and ncRNA function [J].
Cheng, Liang ;
Hu, Yang ;
Sun, Jie ;
Zhou, Meng ;
Jiang, Qinghua .
BIOINFORMATICS, 2018, 34 (11) :1953-1956
[7]   YM500v3: a database for small RNA sequencing in human cancer research [J].
Chung, I-Fang ;
Chang, Shing-Jyh ;
Chen, Chen-Yang ;
Liu, Shu-Hsuan ;
Li, Chia-Yang ;
Chan, Chia-Hao ;
Shih, Chuan-Chi ;
Cheng, Wei-Chung .
NUCLEIC ACIDS RESEARCH, 2017, 45 (D1) :D925-D931
[8]   RNA-Targeted Therapeutics [J].
Crooke, Stanley T. ;
Witztum, Joseph L. ;
Bennett, C. Frank ;
Baker, Brenda F. .
CELL METABOLISM, 2018, 27 (04) :714-739
[9]   MNDR v2.0: an updated resource of ncRNA-disease associations in mammals [J].
Cui, Tianyu ;
Zhang, Lin ;
Huang, Yan ;
Yi, Ying ;
Tan, Puwen ;
Zhao, Yue ;
Hu, Yongfei ;
Xu, Liyan ;
Li, Enmin ;
Wang, Dong .
NUCLEIC ACIDS RESEARCH, 2018, 46 (D1) :D371-D374
[10]   ncDR: a comprehensive resource of non-coding RNAs involved in drug resistance [J].
Dai, Enyu ;
Yang, Feng ;
Wang, Jing ;
Zhou, Xu ;
Song, Qian ;
An, Weiwei ;
Wang, Lihong ;
Jiang, Wei .
BIOINFORMATICS, 2017, 33 (24) :4010-4011