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

查看全文 作　　者：Jingxue [1,6,7]Xin;Junjun [2]Hao;Lang [1]Chen;Tao [3]Zhang;Lei [1,5,7]Li;Luonan [3,5]Chen;Wenmin [4]Zhao;Xuemei [2,5]Lu;Peng [2,5]Shi;Yong [1,5,7]Wang 机构地区：[1]CEMS,NCMIS,MDIS,Academy of Mathematics and Systems Science,Chinese Academy of Sciences,Beijing 100190,China;[2]State Key Laboratory of Genetic Resources and Evolution,Laboratory of Evolutionary and Functional Genomics,Kunming Institute of Zoology,Chinese Academy of Sciences,Kunming 650223,China;[3]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,Shanghai 200031,China;[4]Beijing Institute of Genomics,Chinese Academy of Sciences,Beijing 100101,China;[5]Center for Excellence in Animal Evolution and Genetics,Chinese Academy of Sciences,Kunming 650223,China;[6]Department of Statistics,Department of Biomedical Data Science,Bio-X Program,Stanford University,Stanford,CA 94305,USA;[7]University of Chinese Academy of Sciences,Beijing 100049,China 出　　处：《Quantitative Biology》索引2020年第8卷第1期,共8页 基　　金：ZokorDB is supported by the Strategic Priority Research Program of the Chinese Academy of Sciences(No.XDB13000000);The authors are also supported by the National Natural Science Foundation of China(NSFC)(Nos.11871463,11871462,61671444 and 61621003);We thank all the lab members for discussions on data collection,genome alignment,annotation,GRN reconstruction;We thank Dr.Yilei Wu and his group for help on database design and management. 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