KMS Of Academy of mathematics and systems sciences, CAS
| zokordbtissuespecificregulatorynetworkannotationfornoncodingelementsofplateauzokor | |
Xin Jingxue1; Hao Junjun2; Chen Lang1; Zhang Tao3; Li Lei1; Chen Luonan3; Zhao Wenmin4; Lu Xuemei2; Shi Peng2; Wang Yong1
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| 2020 | |
| Source Publication | quantitativebiology
 |
| ISSN | 2095-4689 |
| Volume | 8Issue:1Pages:43-50 |
| 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/). |
| Keyword | tissue specific regulatory network non-coding element plateau zokor non-model species |
| DOI | 10.1007/s40484-020-0195-4 |
| Indexed By | CSCD |
| Language | 英语 |
| CSCD ID | CSCD:6704248 |
| Citation statistics | |
| Document Type | 期刊论文 |
| Identifier | http://ir.amss.ac.cn/handle/2S8OKBNM/51594 |
| Collection | 应用数学研究所 |
| Affiliation | 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 |
| 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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