التفاصيل البيبلوغرافية
| العنوان: |
ChIP-Hub provides an integrative platform for exploring plant regulome. |
| المؤلفون: |
Fu, Liang-Yu, Zhu, Tao, Zhou, Xinkai, Yu, Ranran, He, Zhaohui, Zhang, Peijing, Wu, Zhigui, Chen, Ming, Kaufmann, Kerstin, Chen, Dijun |
| المصدر: |
Nature Communications; 6/14/2022, Vol. 13 Issue 1, p1-15, 15p |
| مصطلحات موضوعية: |
COMPARATIVE method, GENE regulatory networks, COMPARATIVE genomics, PLANT genomes, PLANT species, CHROMATIN, DATA quality |
| مستخلص: |
Plant genomes encode a complex and evolutionary diverse regulatory grammar that forms the basis for most life on earth. A wealth of regulome and epigenome data have been generated in various plant species, but no common, standardized resource is available so far for biologists. Here, we present ChIP-Hub, an integrative web-based platform in the ENCODE standards that bundles >10,000 publicly available datasets reanalyzed from >40 plant species, allowing visualization and meta-analysis. We manually curate the datasets through assessing ~540 original publications and comprehensively evaluate their data quality. As a proof of concept, we extensively survey the co-association of different regulators and construct a hierarchical regulatory network under a broad developmental context. Furthermore, we show how our annotation allows to investigate the dynamic activity of tissue-specific regulatory elements (promoters and enhancers) and their underlying sequence grammar. Finally, we analyze the function and conservation of tissue-specific promoters, enhancers and chromatin states using comparative genomics approaches. Taken together, the ChIP-Hub platform and the analysis results provide rich resources for deep exploration of plant ENCODE. ChIP-Hub is available at https://biobigdata.nju.edu.cn/ChIPHubTest/. A comprehensive data portal to explore plant regulomes is still unavailable. Here, the authors develop a web-based platform ChIP-Hub in the ENCODE standards and demonstrate its applications in the identification of hierarchical regulatory network, tissue-specific chromatin dynamics, putative enhancers and chromatin states. [ABSTRACT FROM AUTHOR] |
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| قاعدة البيانات: |
Complementary Index |
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