LncPheDB: a genome-wide lncRNAs regulated phenotypes database in plants
LncPheDB (https://www.lncphedb.com/) is a systematic resource of genome-wide long non-coding RNAs (lncRNAs)-phenotypes associations for multiple species. It was established to display the genome-wide lncRNA annotations, target genes prediction, variant-trait associations, gene-phenotype correlations...
| Autores principales: | , , , , , , , , , , , , , , |
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| Formato: | Journal Article |
| Lenguaje: | Inglés |
| Publicado: |
Springer
2022
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| Materias: | |
| Acceso en línea: | https://hdl.handle.net/10568/164025 |
| _version_ | 1855532828558622720 |
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| author | Lou, Danjing Li, Fei Ge, Jinyue Fan, Weiya Liu, Ziran Wang, Yanyan Huang, Jingfen Xing, Meng Guo, Wenlong Wang, Shizhuang Qiao, Weihua Han, Zhenyun Qian, Qian Yang, Qingwen Zheng, Xiaoming |
| author_browse | Fan, Weiya Ge, Jinyue Guo, Wenlong Han, Zhenyun Huang, Jingfen Li, Fei Liu, Ziran Lou, Danjing Qian, Qian Qiao, Weihua Wang, Shizhuang Wang, Yanyan Xing, Meng Yang, Qingwen Zheng, Xiaoming |
| author_facet | Lou, Danjing Li, Fei Ge, Jinyue Fan, Weiya Liu, Ziran Wang, Yanyan Huang, Jingfen Xing, Meng Guo, Wenlong Wang, Shizhuang Qiao, Weihua Han, Zhenyun Qian, Qian Yang, Qingwen Zheng, Xiaoming |
| author_sort | Lou, Danjing |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | LncPheDB (https://www.lncphedb.com/) is a systematic resource of genome-wide long non-coding RNAs (lncRNAs)-phenotypes associations for multiple species. It was established to display the genome-wide lncRNA annotations, target genes prediction, variant-trait associations, gene-phenotype correlations, lncRNA-phenotype correlations, and the similar non-coding regions of the queried sequence in multiple species. LncPheDB sorted out a total of 203,391 lncRNA sequences, 2000 phenotypes, and 120,271 variants of nine species (Zea mays L., Gossypium barbadense L., Triticum aestivum L., Lycopersicon esculentum Mille, Oryza sativa L., Hordeum vulgare L., Sorghum bicolor L., Glycine max L., and Cucumis sativus L.). By exploring the relationship between lncRNAs and the genomic position of variants in genome-wide association analysis, a total of 68,862 lncRNAs were found to be related to the diversity of agronomic traits. More importantly, to facilitate the study of the functions of lncRNAs, we analyzed the possible target genes of lncRNAs, constructed a blast tool for performing similar fragmentation studies in all species, linked the pages of phenotypic studies related to lncRNAs that possess similar fragments and constructed their regulatory networks. In addition, LncPheDB also provides a user-friendly interface, a genome visualization platform, and multi-level and multi-modal convenient data search engine. We believe that LncPheDB plays a crucial role in mining lncRNA-related plant data. |
| format | Journal Article |
| id | CGSpace164025 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2022 |
| publishDateRange | 2022 |
| publishDateSort | 2022 |
| publisher | Springer |
| publisherStr | Springer |
| record_format | dspace |
| spelling | CGSpace1640252024-12-19T14:13:06Z LncPheDB: a genome-wide lncRNAs regulated phenotypes database in plants Lou, Danjing Li, Fei Ge, Jinyue Fan, Weiya Liu, Ziran Wang, Yanyan Huang, Jingfen Xing, Meng Guo, Wenlong Wang, Shizhuang Qiao, Weihua Han, Zhenyun Qian, Qian Yang, Qingwen Zheng, Xiaoming plant science genetics agronomy and crop science biochemistry genetics and molecular biology (miscellaneous) molecular biology biotechnology LncPheDB (https://www.lncphedb.com/) is a systematic resource of genome-wide long non-coding RNAs (lncRNAs)-phenotypes associations for multiple species. It was established to display the genome-wide lncRNA annotations, target genes prediction, variant-trait associations, gene-phenotype correlations, lncRNA-phenotype correlations, and the similar non-coding regions of the queried sequence in multiple species. LncPheDB sorted out a total of 203,391 lncRNA sequences, 2000 phenotypes, and 120,271 variants of nine species (Zea mays L., Gossypium barbadense L., Triticum aestivum L., Lycopersicon esculentum Mille, Oryza sativa L., Hordeum vulgare L., Sorghum bicolor L., Glycine max L., and Cucumis sativus L.). By exploring the relationship between lncRNAs and the genomic position of variants in genome-wide association analysis, a total of 68,862 lncRNAs were found to be related to the diversity of agronomic traits. More importantly, to facilitate the study of the functions of lncRNAs, we analyzed the possible target genes of lncRNAs, constructed a blast tool for performing similar fragmentation studies in all species, linked the pages of phenotypic studies related to lncRNAs that possess similar fragments and constructed their regulatory networks. In addition, LncPheDB also provides a user-friendly interface, a genome visualization platform, and multi-level and multi-modal convenient data search engine. We believe that LncPheDB plays a crucial role in mining lncRNA-related plant data. 2022-10-05 2024-12-19T12:53:20Z 2024-12-19T12:53:20Z Journal Article https://hdl.handle.net/10568/164025 en Open Access Springer Lou, Danjing; Li, Fei; Ge, Jinyue; Fan, Weiya; Liu, Ziran; Wang, Yanyan; Huang, Jingfen; Xing, Meng; Guo, Wenlong; Wang, Shizhuang; Qiao, Weihua; Han, Zhenyun; Qian, Qian; Yang, Qingwen and Zheng, Xiaoming. 2022. LncPheDB: a genome-wide lncRNAs regulated phenotypes database in plants. aBIOTECH, Volume 3 no. 3 p. 169-177 |
| spellingShingle | plant science genetics agronomy and crop science biochemistry genetics and molecular biology (miscellaneous) molecular biology biotechnology Lou, Danjing Li, Fei Ge, Jinyue Fan, Weiya Liu, Ziran Wang, Yanyan Huang, Jingfen Xing, Meng Guo, Wenlong Wang, Shizhuang Qiao, Weihua Han, Zhenyun Qian, Qian Yang, Qingwen Zheng, Xiaoming LncPheDB: a genome-wide lncRNAs regulated phenotypes database in plants |
| title | LncPheDB: a genome-wide lncRNAs regulated phenotypes database in plants |
| title_full | LncPheDB: a genome-wide lncRNAs regulated phenotypes database in plants |
| title_fullStr | LncPheDB: a genome-wide lncRNAs regulated phenotypes database in plants |
| title_full_unstemmed | LncPheDB: a genome-wide lncRNAs regulated phenotypes database in plants |
| title_short | LncPheDB: a genome-wide lncRNAs regulated phenotypes database in plants |
| title_sort | lncphedb a genome wide lncrnas regulated phenotypes database in plants |
| topic | plant science genetics agronomy and crop science biochemistry genetics and molecular biology (miscellaneous) molecular biology biotechnology |
| url | https://hdl.handle.net/10568/164025 |
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