zokordbtissuespecificregulatorynetworkannotationfornoncodingelementsofplateauzokor

doi:10.1007/s40484-020-0195-4

CSpace > 应用数学研究所

	zokordbtissuespecificregulatorynetworkannotationfornoncodingelementsofplateauzokor
	Xin Jingxue 1; Hao Junjun 2; Chen Lang 1; Zhang Tao 3; Li Lei 1; Chen Luonan 3; Zhao Wenmin 4; Lu Xuemei 2; Shi Peng 2; Wang Yong1
	2020
发表期刊	quantitativebiology
ISSN	2095-4689
卷号	8 期号:1 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 environment 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), 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. 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
DOI	10.1007/s40484-020-0195-4
收录类别	CSCD
语种	英语
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/51594
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.中国科学院动物研究所 3.Institute of Biochemistry and Cell Biology,Shanghai Institutes for Biological Sciences,Chinese Academy of Sciences 4.中国科学院北京基因组研究所
推荐引用方式 GB/T 7714	Xin Jingxue,Hao Junjun,Chen Lang,et al. zokordbtissuespecificregulatorynetworkannotationfornoncodingelementsofplateauzokor[J]. quantitativebiology,2020,8(1):43-50.
APA	Xin Jingxue.,Hao Junjun.,Chen Lang.,Zhang Tao.,Li Lei.,...&Wang Yong.(2020).zokordbtissuespecificregulatorynetworkannotationfornoncodingelementsofplateauzokor.quantitativebiology,8(1),43-50.
MLA	Xin Jingxue,et al."zokordbtissuespecificregulatorynetworkannotationfornoncodingelementsofplateauzokor".quantitativebiology 8.1(2020):43-50.