LjaFGD: Lonicera japonica functional genomics database

Autor:	Wenying Xu, Zhongqiu Li, Qiaoqiao Xiao, Mengmeng Qu, Zhen Su, Jiaotong Yang
Rok vydání:	2021
Předmět:	0106 biological sciences 0301 basic medicine Plant Science computer.software_genre 01 natural sciences Biochemistry Genome General Biochemistry Genetics and Molecular Biology Japonica 03 medical and health sciences Gene Expression Regulation Plant Databases Genetic Flavonol synthase Gene Regulatory Networks MYB Luteolin Gene Base Sequence biology Functional analysis Database food and beverages Molecular Sequence Annotation Genomics biology.organism_classification Biosynthetic Pathways Lonicera 030104 developmental biology biology.protein Chlorogenic Acid Functional genomics computer Function (biology) 010606 plant biology & botany
Zdroj:	Journal of Integrative Plant Biology. 63:1422-1436
ISSN:	1744-7909 1672-9072
Popis:	Lonicera japonica Thunb., a traditional Chinese herb, has been used for treating human diseases for thousands of years. Recently, the genome of L. japonica has been decoded, providing valuable information for research into gene function. However, no comprehensive database for gene functional analysis and mining is available for L. japonica. We therefore constructed LjaFGD (www.gzybioinformatics.cn/LjaFGD and bioinformatics.cau.edu.cn/LjaFGD), a database for analyzing and comparing gene function in L. japonica. We constructed a gene co-expression network based on 77 RNA-seq samples, and then annotated genes of L. japonica by alignment against protein sequences from public databases. We also introduced several tools for gene functional analysis, including Blast, motif analysis, gene set enrichment analysis, heatmap analysis, and JBrowse. Our co-expression network revealed that MYB and WRKY transcription factor family genes were co-expressed with genes encoding key enzymes in the biosynthesis of chlorogenic acid and luteolin in L. japonica. We used flavonol synthase 1 (LjFLS1) as an example to show the reliability and applicability of our database. LjaFGD and its various associated tools will provide researchers with an accessible platform for retrieving functional information on L. japonica genes to further biological discovery.
Databáze:	OpenAIRE
Externí odkaz:	https://explore.openaire.eu/search/publication?articleId=doi_dedup___::e0a07f66cb7f10aebaba954ee939ecc6 https://doi.org/10.1111/jipb.13112 Zobrazit plný text záznamu Plný text ve formátu PDF Plný text ve formátu HTML
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