KMS Of Academy of mathematics and systems sciences, CAS
| ZokorDB: tissue specific regulatory network annotation for non-coding elements of plateau zokor | |
Jingxue Xin1; Junjun Hao4; Lang Chen1; Tao Zhang5; Lei Li1; Luonan Chen5; Wenmin Zhao7; Xuemei Lu4; Peng Shi4; Yong Wang1
| |
| 2020 | |
| Source Publication | 定量生物学:英文版
 |
| ISSN | 2095-4689 |
| Volume | 8.0Issue:1.0Pages:43-50 |
| Abstract | 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/). |
| Keyword | tissue specific regulatory network non-coding element plateau zokor non-model species |
| Indexed By | CSCD |
| Language | 中文 |
| CSCD ID | CSCD:6704248 |
| Citation statistics | |
| Document Type | 期刊论文 |
| Identifier | http://ir.amss.ac.cn/handle/2S8OKBNM/54622 |
| Collection | 应用数学研究所 |
| Affiliation | 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 |
| Recommended Citation 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. |
| Files in This Item: | There are no files associated with this item. | |||||
Items in the repository are protected by copyright, with all rights reserved, unless otherwise indicated.
Edit Comment