TY - JOUR
T1 - MaGenDB
T2 - A functional genomics hub for Malvaceae plants
AU - Wang, Dehe
AU - Fan, Weiliang
AU - Guo, Xiaolong
AU - Wu, Kai
AU - Zhou, Siyu
AU - Chen, Zonggui
AU - Li, Danyang
AU - Wang, Kun
AU - Zhu, Yuxian
AU - Zhou, Yu
N1 - Publisher Copyright:
© 2019 The Author(s). Published by Oxford University Press on behalf of Nucleic Acids Research.
PY - 2020/1/1
Y1 - 2020/1/1
N2 - 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.
AB - 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.
UR - https://www.scopus.com/pages/publications/85077665653
U2 - 10.1093/nar/gkz953
DO - 10.1093/nar/gkz953
M3 - 文章
C2 - 31665439
AN - SCOPUS:85077665653
SN - 0305-1048
VL - 48
SP - D1076-D1084
JO - Nucleic Acids Research
JF - Nucleic Acids Research
IS - D1
ER -