MaGenDB


31665439	MaGenDB: a functional genomics hub for Malvaceae plants. [PMID: 31665439] Wang D, Fan W, Guo X, Wu K, Zhou S, Chen Z, Li D, Wang K, Zhu Y, Zhou Y. Abstract Malvaceae is a family of flowering plants containing many economically important plant species including cotton, cacao and durian. Recently, the genomes of several Malvaceae species have been decoded, and many omics data were generated for individual species. However, no integrative database of multiple species, enabling users to jointly compare and analyse relevant data, is available for Malvaceae. Thus, we developed a user-friendly database named MaGenDB (http://magen.whu.edu.cn) as a functional genomics hub for the plant community. We collected the genomes of 13 Malvaceae species, and comprehensively annotated genes from different perspectives including functional RNA/protein element, gene ontology, KEGG orthology, and gene family. We processed 374 sets of diverse omics data with the ENCODE pipelines and integrated them into a customised genome browser, and designed multiple dynamic charts to present gene/RNA/protein-level knowledge such as dynamic expression profiles and functional elements. We also implemented a smart search system for efficiently mining genes. In addition, we constructed a functional comparison system to help comparative analysis between genes on multiple features in one species or across closely related species. This database and associated tools will allow users to quickly retrieve large-scale functional information for biological discovery. Nucleic Acids Res. 2020:48(D1) \| 23 Citations (from Europe PMC, 2025-03-22)

MaGenDB: a functional genomics hub for Malvaceae plants. [PMID: 31665439]

Wang D, Fan W, Guo X, Wu K, Zhou S, Chen Z, Li D, Wang K, Zhu Y, Zhou Y.

Malvaceae is a family of flowering plants containing many economically important plant species including cotton, cacao and durian. Recently, the genomes of several Malvaceae species have been decoded, and many omics data were generated for individual species. However, no integrative database of multiple species, enabling users to jointly compare and analyse relevant data, is available for Malvaceae. Thus, we developed a user-friendly database named MaGenDB (http://magen.whu.edu.cn) as a functional genomics hub for the plant community. We collected the genomes of 13 Malvaceae species, and comprehensively annotated genes from different perspectives including functional RNA/protein element, gene ontology, KEGG orthology, and gene family. We processed 374 sets of diverse omics data with the ENCODE pipelines and integrated them into a customised genome browser, and designed multiple dynamic charts to present gene/RNA/protein-level knowledge such as dynamic expression profiles and functional elements. We also implemented a smart search system for efficiently mining genes. In addition, we constructed a functional comparison system to help comparative analysis between genes on multiple features in one species or across closely related species. This database and associated tools will allow users to quickly retrieve large-scale functional information for biological discovery.

Nucleic Acids Res. 2020:48(D1) | 23 Citations (from Europe PMC, 2025-03-22)

URL:	http://magen.whu.edu.cn
Full name:	A user-friendly omics database of Malvaceae species
Description:	MaGenDB collected all available genomes of Malvaceae(family of flowering plants containing many economically important plant species), comprehensively annotated genes from different perspectives including functional RNA/protein element, gene ontology, KEGG orthology, and gene family.
Year founded:	2020
Last update:
Version:
Accessibility:	Accessible
Country/Region:	China

Data type:	DNA Protein RNA
Data object:	Plant
Database category:	Gene genome and annotation
Major species:	Bombax ceiba Durio zibethinus Gossypium arboreum Gossypium barbadense Gossypium hirsutum Gossypium raimondii Theobroma cacao Herrania umbratica Corchorus capsularis Corchorus olitorius Gossypioides kirkii Hibiscus syriacus Kokia drynarioides
Keywords:	omics data functional RNA/protein element gene ontology KEGG orthology gene family

University/Institution:	Wuhan University
Address:	College of Life Sciences Wuhan University Luojia Hill, Wuhan 430072 P.R. China
City:	Wuhan
Province/State:	Hubei
Country/Region:	China
Contact name (PI/Team):	Dr. Yu Zhou
Contact email (PI/Helpdesk):	yu.zhou@whu.edu.cn

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Database Commons a catalog of worldwide biological databases