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. 2022 Oct 5;3(3):169-177.
doi: 10.1007/s42994-022-00084-3. eCollection 2022 Sep.

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

Danjing Lou  1 , Fei Li  1 , Jinyue Ge  1 , Weiya Fan  1 , Ziran Liu  2 , Yanyan Wang  1 , Jingfen Huang  1 , Meng Xing  1 , Wenlong Guo  1 , Shizhuang Wang  1 , Weihua Qiao  1   3 , Zhenyun Han  1 , Qian Qian  1   4   5 , Qingwen Yang  1   3 , Xiaoming Zheng  1   3   6
Affiliations

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

Danjing Lou et al. aBIOTECH. .

Abstract

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.

Supplementary information: The online version contains supplementary material available at 10.1007/s42994-022-00084-3.

Keywords: GWAS; LncRNA; Phenotype; Plants; SNP.

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Conflict of interest statement

Conflict of interestAuthor declares no conflicts of interests.

Figures

Fig. 1
Fig. 1
Data processing workflow and outcomes of LncPheDB. A The nine species included in the database. B The data processing workflow of lncRNA and the curation process adopted by the GWAS is on the right. C Summary of the data contained in LncPheDB. D Database statistics in this study
Fig. 2
Fig. 2
Database contents and functions of LncPheDB
See this image and copyright information in PMC

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