HERB: a high-throughput experiment- and reference-guided database of traditional Chinese medicine

doi:10.1093/nar/gkaa1063

	HERB: a high-throughput experiment- and reference-guided database of traditional Chinese medicine
	Fang, ShuangSang 1; Dong, Lei 1; Liu, Liu 1; Guo, JinCheng 1; Zhao, LianHe 2; Zhang, JiaYuan 1; Bu, DeChao 2; Liu, XinKui 1; Huo, PeiPei 2; Cao, WanChen 1; Dong, QiongYe 2; Wu, JiaRui 1; Zeng, Xiaoxi 3; Wu, Yang 2; Zhao, Yi 1,2
	2021-01-08
发表期刊	NUCLEIC ACIDS RESEARCH
ISSN	0305-1048
卷号	49 期号:D1 页码:D1197-D1206
摘要	Pharmacotranscriptomics has become a powerful approach for evaluating the therapeutic efficacy of drugs and discovering new drug targets. Recently, studies of traditional Chinese medicine (TCM) have increasingly turned to high-throughput transcriptomic screens for molecular effects of herbs/ingredients. And numerous studies have examined gene targets for herbs/ingredients, and link herbs/ingredients to various modern diseases. However, there is currently no systematic database organizing these data for TCM. Therefore, we built HERB, a high-throughput experiment- and reference-guided database of TCM, with its Chinese name as Ben-CaoZuJian. We re-analyzed 6164 gene expression profiles from1037 high-throughput experiments evaluating TCM herbs/ingredients, and generated connections between TCM herbs/ingredients and 2837 modern drugs by mapping the comprehensive pharmacotranscriptomics dataset in HERB to CMap, the largest such dataset for modern drugs. Moreover, we manually curated 1241 gene targets and 494 modern diseases for 473 herbs/ingredients from 1966 references published recently, and cross-referenced this novel information to databases containing such data for drugs. Together with database mining and statistical inference, we linked 12 933 targets and 28 212 diseases to 7263 herbs and 49 258 ingredients and provided six pairwise relationships among them in HERB. In summary, HERB will intensively support the modernization of TCM and guide rational modern drug discovery efforts.
DOI	10.1093/nar/gkaa1063
收录类别	SCI
语种	英语
资助项目	National Key R&D Program of China[2018YFC17041 00] ; National Key R&D Program of China[2019YFC1709801] ; National Key R&D Program of China[2018YFC1313000] ; National Key R&D Program of China[2018YFC13130 01] ; National Key R&D Program of China[2018YFD1000604] ; National Key R&D Program of China[2018YFC1704106] ; National Natural Science Foundation for Young Scholars of China[31701141] ; National Natural Science Foundation for Young Scholars of China[31701149] ; National Natural Science Foundation of China[91740113] ; National Natural Science Foundation of China[32070670] ; Zhejiang Provincial Natural Science Foundation of China[LY21C060003] ; BMICC of National Population Health Data Center ; Innovation Project for Institute of Computing Technology, CAS[20186060] ; China Postdoctoral Science Foundation[2019M660033] ; China Postdoctoral Innovative Talent Foundation[BX20200068]
WOS研究方向	Biochemistry & Molecular Biology
WOS类目	Biochemistry & Molecular Biology
WOS记录号	WOS:000608437800147
出版者	OXFORD UNIV PRESS
引用统计	被引频次：255[WOS] [WOS记录] [WOS相关记录]
文献类型	期刊论文
条目标识符	http://119.78.100.204/handle/2XEOYT63/16481
专题	中国科学院计算技术研究所期刊论文_英文
通讯作者	Wu, Yang; Zhao, Yi
作者单位	1.Beijing Univ Chinese Med, Beijing 100029, Peoples R China 2.Chinese Acad Sci, Adv Comp Res Ctr, Inst Comp Technol, Key Lab Intelligent Informat Proc, Beijing 100190, Peoples R China 3.Sichuan Univ, West China Biomed Big Data Ctr, Kidney Res Inst, Div Nephrol,West China Hosp, Chengdu 610041, Peoples R China
推荐引用方式 GB/T 7714	Fang, ShuangSang,Dong, Lei,Liu, Liu,et al. HERB: a high-throughput experiment- and reference-guided database of traditional Chinese medicine[J]. NUCLEIC ACIDS RESEARCH,2021,49(D1):D1197-D1206.
APA	Fang, ShuangSang.,Dong, Lei.,Liu, Liu.,Guo, JinCheng.,Zhao, LianHe.,...&Zhao, Yi.(2021).HERB: a high-throughput experiment- and reference-guided database of traditional Chinese medicine.NUCLEIC ACIDS RESEARCH,49(D1),D1197-D1206.
MLA	Fang, ShuangSang,et al."HERB: a high-throughput experiment- and reference-guided database of traditional Chinese medicine".NUCLEIC ACIDS RESEARCH 49.D1(2021):D1197-D1206.