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
	Xin, Jingxue; Hao, Junjun; Chen, Lang; Zhang, Tao; Li, Lei; Chen, Luonan; Zhao, Wenmin; Lu, Xuemei; Shi, Peng; Wang, Yong
	2020
发表期刊	Quantitative Biology
ISSN	2095-4689
卷号	8 期号:1 页码:43-50
摘要	BackgroundPlateau zokor inhabits in sealed burrows from 2,000 to 4,200 meters at Qinghai-Tibet Plateau. This extreme living environment makes it a great model to study animal adaptation to hypoxia, low temperature, and high carbon dioxide concentration.MethodsWe 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.ResultsZokorDB provides a general draft gene regulatory network (GRN), i.e., 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.ConclusionsA 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/).
收录类别	sci
语种	英语
文献类型	期刊论文
条目标识符	http://ir.kiz.ac.cn/handle/152453/12824
专题	科研部门_进化与功能基因组学（施鹏）遗传资源与进化国家重点实验室
推荐引用方式 GB/T 7714	Xin, Jingxue,Hao, Junjun,Chen, Lang,et al. ZokorDB: tissue specific regulatory network annotation for non-coding elements of plateau zokor[J]. Quantitative Biology,2020,8(1):43-50.
APA	Xin, Jingxue.,Hao, Junjun.,Chen, Lang.,Zhang, Tao.,Li, Lei.,...&Wang, Yong.(2020).ZokorDB: tissue specific regulatory network annotation for non-coding elements of plateau zokor.Quantitative Biology,8(1),43-50.
MLA	Xin, Jingxue,et al."ZokorDB: tissue specific regulatory network annotation for non-coding elements of plateau zokor".Quantitative Biology 8.1(2020):43-50.

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2021110104.pdf（887KB）	期刊论文	出版稿	开放获取	CC BY-NC-SA	请求全文