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| Auteurs principaux: | , , , , , , , , , |
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| Format: | Artículo científico |
| Langue: | en |
| Publié: |
Plant, cell & environment
2025
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| Sujets: | |
| Accès en ligne: | https://pubmed.ncbi.nlm.nih.gov/39660842/ |
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| _version_ | 1868266270311317504 |
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| author | Xu, Chaoqun Song, Ling-Yu Li, Jing Zhang, Lu-Dan Guo, Ze-Jun Ma, Dong-Na Dai, Ming-Jin Li, Qing-Hua Liu, Jin-Yu Zheng, Hai-Lei |
| author_facet | Xu, Chaoqun Song, Ling-Yu Li, Jing Zhang, Lu-Dan Guo, Ze-Jun Ma, Dong-Na Dai, Ming-Jin Li, Qing-Hua Liu, Jin-Yu Zheng, Hai-Lei Xu, Chaoqun Song, Ling-Yu Li, Jing Zhang, Lu-Dan Guo, Ze-Jun Ma, Dong-Na Dai, Ming-Jin Li, Qing-Hua Liu, Jin-Yu Zheng, Hai-Lei |
| collection | PubMed - marine biology |
| contents | MangroveDB: A Comprehensive Online Database for Mangroves Based on Multi-Omics Data. Xu, Chaoqun Song, Ling-Yu Li, Jing Zhang, Lu-Dan Guo, Ze-Jun Ma, Dong-Na Dai, Ming-Jin Li, Qing-Hua Liu, Jin-Yu Zheng, Hai-Lei Databases, Genetic Transcriptome Genomics Wetlands Computational Biology Gene Expression Profiling Internet Avicennia Genome, Plant Rhizophoraceae Multiomics Mangroves are dominant flora of intertidal zones along tropical and subtropical coastline around the world that offer important ecological and economic value. Recently, the genomes of mangroves have been decoded, and massive omics data were generated and deposited in the public databases. Reanalysis of multi-omics data can provide new biological insights excluded in the original studies. However, the requirements for computational resource and lack of bioinformatics skill for experimental researchers limit the effective use of the original data. To fill this gap, we uniformly processed 942 transcriptome data, 386 whole-genome sequencing data, and provided 13 reference genomes and 40 reference transcriptomes for 53 mangroves. Finally, we built an interactive web-based database platform MangroveDB (https://github.com/Jasonxu0109/MangroveDB), which was designed to provide comprehensive gene expression datasets to facilitate their exploration and equipped with several online analysis tools, including principal components analysis, differential gene expression analysis, tissue-specific gene expression analysis, GO and KEGG enrichment analysis. MangroveDB not only provides query functions about genes annotation, but also supports some useful visualization functions for analysis results, such as volcano plot, heatmap, dotplot, PCA plot, bubble plot, population structure, and so on. In conclusion, MangroveDB is a valuable resource for the mangroves research community to efficiently use the massive public omics datasets. |
| format | Artículo científico |
| id | pubmed_39660842 |
| institution | PubMed |
| language | en |
| publishDate | 2025 |
| publisher | Plant, cell & environment |
| record_format | pubmed |
| spellingShingle | MangroveDB: A Comprehensive Online Database for Mangroves Based on Multi-Omics Data. Xu, Chaoqun Song, Ling-Yu Li, Jing Zhang, Lu-Dan Guo, Ze-Jun Ma, Dong-Na Dai, Ming-Jin Li, Qing-Hua Liu, Jin-Yu Zheng, Hai-Lei Databases, Genetic Transcriptome Genomics Wetlands Computational Biology Gene Expression Profiling Internet Avicennia Genome, Plant Rhizophoraceae Multiomics MangroveDB: A Comprehensive Online Database for Mangroves Based on Multi-Omics Data. Xu, Chaoqun Song, Ling-Yu Li, Jing Zhang, Lu-Dan Guo, Ze-Jun Ma, Dong-Na Dai, Ming-Jin Li, Qing-Hua Liu, Jin-Yu Zheng, Hai-Lei Databases, Genetic Transcriptome Genomics Wetlands Computational Biology Gene Expression Profiling Internet Avicennia Genome, Plant Rhizophoraceae Multiomics Mangroves are dominant flora of intertidal zones along tropical and subtropical coastline around the world that offer important ecological and economic value. Recently, the genomes of mangroves have been decoded, and massive omics data were generated and deposited in the public databases. Reanalysis of multi-omics data can provide new biological insights excluded in the original studies. However, the requirements for computational resource and lack of bioinformatics skill for experimental researchers limit the effective use of the original data. To fill this gap, we uniformly processed 942 transcriptome data, 386 whole-genome sequencing data, and provided 13 reference genomes and 40 reference transcriptomes for 53 mangroves. Finally, we built an interactive web-based database platform MangroveDB (https://github.com/Jasonxu0109/MangroveDB), which was designed to provide comprehensive gene expression datasets to facilitate their exploration and equipped with several online analysis tools, including principal components analysis, differential gene expression analysis, tissue-specific gene expression analysis, GO and KEGG enrichment analysis. MangroveDB not only provides query functions about genes annotation, but also supports some useful visualization functions for analysis results, such as volcano plot, heatmap, dotplot, PCA plot, bubble plot, population structure, and so on. In conclusion, MangroveDB is a valuable resource for the mangroves research community to efficiently use the massive public omics datasets. |
| title | MangroveDB: A Comprehensive Online Database for Mangroves Based on Multi-Omics Data. |
| topic | Databases, Genetic Transcriptome Genomics Wetlands Computational Biology Gene Expression Profiling Internet Avicennia Genome, Plant Rhizophoraceae Multiomics |
| url | https://pubmed.ncbi.nlm.nih.gov/39660842/ |