期刊
NATURE COMMUNICATIONS
卷 13, 期 1, 页码 -出版社
NATURE PORTFOLIO
DOI: 10.1038/s41467-022-30770-1
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资金
- Center for Information Technology
- High Performance Computing Center of Nanjing University
- National Natural Science Foundation of China [32070656]
- Nanjing University Deng Feng Scholars Program
- Priority Academic Program Development (PAPD) of Jiangsu Higher Education Institutions
- Alexander-von-Humboldt foundation
- Federal Ministry of Education and Research
- 2022 Postgraduate Research & Practice Innovation Program of Jiangsu Province [KYCX22_0118]
- Fundamental Research Funds for the Central Universities
- Collaborative Innovation Center for Modern Crop Production
- Ministry
- Open Access Publication Fund of Humboldt-Universitat zu Berlin
ChIP-Hub is an integrated web platform that provides rich resources of plant regulome and epigenome data for visualization and meta-analysis. By manually curating and evaluating the data quality, it allows in-depth investigation of the co-association of different regulators and the dynamic activity of tissue-specific regulatory elements.
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 similar to 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/ChIPHub/.
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