LncPheDB: a genome-wide lncRNAs regulated phenotypes database in plants

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dc.creatorLou, Danjing
dc.creatorLi, Fei
dc.creatorGe, Jinyue
dc.creatorFan, Weiya
dc.creatorLiu, Ziran
dc.creatorWang, Yanyan
dc.creatorHuang, Jingfen
dc.creatorXing, Meng
dc.creatorGuo, Wenlong
dc.creatorWang, Shizhuang
dc.creatorQiao, Weihua
dc.creatorHan, Zhenyun
dc.creatorQian, Qian
dc.creatorYang, Qingwen
dc.creatorZheng, Xiaoming
dc.date2022-10-05
dc.date2024-12-19T12:53:20Z
dc.date2024-12-19T12:53:20Z
dc.date.accessioned2026-06-27T04:13:02Z
dc.descriptionLncPheDB (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.
dc.identifierhttps://hdl.handle.net/10568/164025
dc.identifier.urihttp://hdl.handle.net/123456789/25430
dc.languageen
dc.publisherSpringer
dc.rightsOpen Access
dc.sourceLou, 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
dc.subjectplant science
dc.subjectgenetics
dc.subjectagronomy and crop science
dc.subjectbiochemistry
dc.subjectgenetics and molecular biology (miscellaneous)
dc.subjectmolecular biology
dc.subjectbiotechnology
dc.titleLncPheDB: a genome-wide lncRNAs regulated phenotypes database in plants
dc.typeJournal Article

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Instituto Internacional de Investigación del Arroz (IRRI)