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

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	ZokorDB: tissue specific regulatory network annotation for non-coding elements of plateau zokor
	Jingxue Xin 1; Junjun Hao 4; Lang Chen 1; Tao Zhang 5; Lei Li 1; Luonan Chen 5; Wenmin Zhao 7; Xuemei Lu 4; Peng Shi 4; Yong Wang1
	2020
发表期刊	定量生物学:英文版
ISSN	2095-4689
卷号	8.0 期号:1.0 页码:43-50
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/).
关键词	tissue specific regulatory network non-coding element plateau zokor non-model species
收录类别	CSCD
语种	中文
CSCD记录号	CSCD:6704248
引用统计
文献类型	期刊论文
条目标识符	http://ir.amss.ac.cn/handle/2S8OKBNM/54622
专题	应用数学研究所
作者单位	1.CEMS,NCMIS,MDIS,Academy of Mathematics and Systems Science,Chinese Academy of Sciences 2.Department of Statistics,Department of Biomedical Data Science,Bio-X Program,Stanford University,Stanford,USA 3.中国科学院大学 4.中国科学院动物研究所 5.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 6.Center for Excellence in Animal Evolution and Genetics,Chinese Academy of Sciences 7.中国科学院北京基因组研究所
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.