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ZokorDB: tissue specific regulatory network annotation for non-coding elements of plateau zokor |
Jingxue Xin1,6,7, Junjun Hao2, Lang Chen1, Tao Zhang3, Lei Li1,5,7, Luonan Chen3,5, Wenmin Zhao4, Xuemei Lu2,5, Peng Shi2,5( ), Yong Wang1,5,7( ) |
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 |
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Abstract 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/).
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Keywords
tissue specific regulatory network
non-coding element
plateau zokor
non-model species
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Corresponding Author(s):
Peng Shi,Yong Wang
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Just Accepted Date: 17 January 2020
Online First Date: 05 March 2020
Issue Date: 23 March 2020
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