ZokorDB: tissue specific regulatory network annotation for non-coding elements of plateau zokor

	ZokorDB: tissue specific regulatory network annotation for non-coding elements of plateau zokor
	Jingxue Xin 7; Junjun Hao 3; Lang Chen 7; Tao Zhang 4; Lei Li 7; Luonan Chen 4; Wenmin Zhao 5; Xuemei Lu 3; Peng Shi 3; Yong Wang 7
刊名	定量生物学:英文版
	2020
卷号	8.0 期号:1.0 页码:43-50
关键词	tissue specific regulatory network non-coding element plateau zokor non-model species
ISSN号	2095-4689
英文摘要	Background:Plateau zokor inhabits in sealed burrows from 2,000 to 4,200 meters at Qinghai-Tibet Plateau.This extreme living env ironment makes it a great model to study animal adaptation to hypoxia,low temperature,and high carbon dioxide concentration.Methods:We provide an integrated resource,ZokorDB,for tissue specific regulatory network annotation for zokor.ZokorDB is based on a high-quality draft genome of a plateau zokor at 3,300 m and its transcriptional profiles in brain,heart,liver,kidney,and lung.The conserved non-coding elements of zokor are annotated by their nearest genes and upstream transcriptional factor motif binding sites.Results:ZokorDB provides a general draft gene regulatory network(GRN),Le?potential transcription factor(TF)binds to non-coding regulatory elements and regulates the expression of target genes(TG).Furthermore,we refined the GRN by incorporating matched RNA-seq and DNase-seq data from mouse ENCODE project and reconstructed five tissue-specific regulatory networks.Conclusions:A web-based,open-access database is developed for easily searching,visualizing,and downloading the annotation and data.The pipeline of non-coding region annotation for zokor will be useful for other non-model species.ZokorDB is free available at the website(bigd.big.ac.cn/zokordb/).
语种	中文
CSCD记录号	CSCD:6704248
内容类型	期刊论文
源URL	[http://ir.amss.ac.cn/handle/2S8OKBNM/54621]
专题	中国科学院数学与系统科学研究院
作者单位	1.Department of Statistics,Department of Biomedical Data Science,Bio-X Program,Stanford University,Stanford,USA 2.中国科学院大学 3.中国科学院动物研究所 4.Key Laboratory of Systems Biology,Innovation Center for Cell Signaling Network,Institute of Biochemistry and Cell Biology,Shanghai Institutes for Biological Sciences,Chinese Academy of Sciences 5.中国科学院北京基因组研究所 6.Center for Excellence in Animal Evolution and Genetics,Chinese Academy of Sciences 7.CEMS,NCMIS,MDIS,Academy of Mathematics and Systems Science,Chinese Academy of Sciences
推荐引用方式 GB/T 7714	Jingxue Xin,Junjun Hao,Lang Chen,et al. ZokorDB: tissue specific regulatory network annotation for non-coding elements of plateau zokor[J]. 定量生物学:英文版,2020,8.0(1.0):43-50.
APA	Jingxue Xin.,Junjun Hao.,Lang Chen.,Tao Zhang.,Lei Li.,...&Yong Wang.(2020).ZokorDB: tissue specific regulatory network annotation for non-coding elements of plateau zokor.定量生物学:英文版,8.0(1.0),43-50.
MLA	Jingxue Xin,et al."ZokorDB: tissue specific regulatory network annotation for non-coding elements of plateau zokor".定量生物学:英文版 8.0.1.0(2020):43-50.