LncPheDB:一个全基因组lncRNA调控的植物表型数据库

IF 4.6 4区 农林科学 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY
Danjing Lou, Fei Li, Jinyue Ge, Weiya Fan, Ziran Liu, Yanyan Wang, Jingfen Huang, Meng Xing, Wenlong Guo, Shizhuang Wang, Weihua Qiao, Zhenyun Han, Qian Qian, Qingwen Yang, Xiaoming Zheng
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引用次数: 4

摘要

LncPheDB(https://www.lncphedb.com/)是全基因组长非编码RNA(lncRNA)-多个物种表型关联的系统资源。建立它是为了在多个物种中显示全基因组lncRNA注释、靶基因预测、变异性状关联、基因表型相关性、lncRNA表型相关性以及查询序列的相似非编码区。LncPheDB共筛选出203391个lncRNA序列、2000个表型,和9个种(玉米、棉棉、小麦、番茄、水稻、大麦、高粱、大豆和黄瓜)的120271个变体。通过在全基因组关联分析中探讨lncRNA与变体基因组位置的关系,共发现68862个lncRNA与农艺性状的多样性有关。更重要的是,为了促进lncRNA功能的研究,我们分析了lncRNA可能的靶基因,构建了一个用于在所有物种中进行类似片段研究的爆炸工具,链接了与拥有类似片段的lncRNA相关的表型研究页面,并构建了它们的调控网络。此外,LncPheDB还提供了用户友好的界面、基因组可视化平台和多层次、多模式的便捷数据搜索引擎。我们认为LncPheDB在挖掘lncRNA相关植物数据方面发挥着至关重要的作用。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
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, 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.

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CiteScore
7.70
自引率
2.80%
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