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Xin Jingxue1; Hao Junjun2; Chen Lang1; Zhang Tao3; Li Lei1; Chen Luonan3; Zhao Wenmin4; Lu Xuemei2; Shi Peng2; Wang Yong1
Source Publicationquantitativebiology
AbstractBackground: 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/).
Keywordtissue specific regulatory network non-coding element plateau zokor non-model species
Indexed ByCSCD
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Document Type期刊论文
Affiliation1.CEMS,NCMIS,MDIS,Academy of Mathematics and Systems Science,Chinese Academy of Sciences
3.Institute of Biochemistry and Cell Biology,Shanghai Institutes for Biological Sciences,Chinese Academy of Sciences
Recommended Citation
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.
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