The Rice Online Expression Profiles Array Database Version 2 (ROADv2): An Interactive Atlas for Rice Functional Genomics.

IF 4.8 1区 农林科学 Q1 AGRONOMY Rice Pub Date : 2024-12-26 DOI:10.1186/s12284-024-00753-5
Wonjae Hwang, Woo-Jong Hong, Eui-Jung Kim, Jihye Kim, Sunok Moon, Ki-Hong Jung
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引用次数: 0

Abstract

The Rice Online expression profiles Array Database version 2 (ROADv2; https://roadv2.khu.ac.kr ), an enhanced database for rice gene expression analysis, transitions from the previous microarray platforms to RNA-Seq data for improved accuracy. It encompasses 328 datasets from diverse experimental series, including anatomy, abiotic and biotic stress, hormone response, and nutrient starvation. Key updates include gene annotation (upgraded to RGAP version 7) and functional enrichment data (utilizing recent Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) versions). ROADv2 debuts protein-protein interaction (PPI) network analysis and broadens interactive visualization across all features. Gene expression data are segmented into anatomy, biotic, abiotic, nutrient, and hormone categories, with user-interactive heatmaps displaying normalized log2 expression and log2 fold change data. Coexpression correlation analysis identifies genes with similar patterns, visualized through interactive network graphs. Functional enrichment tools display GO and KEGG analyses with significant terms emphasized in various formats. PPI network analysis integrates coexpression data to enhance prediction accuracy. Validation studies affirm the database's reliability, demonstrating reproducible tissue/organ-specific expression patterns. ROADv2 provides a comprehensive resource for rice functional genomics studies.

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来源期刊
Rice
Rice AGRONOMY-
CiteScore
10.10
自引率
3.60%
发文量
60
审稿时长
>12 weeks
期刊介绍: Rice aims to fill a glaring void in basic and applied plant science journal publishing. This journal is the world''s only high-quality serial publication for reporting current advances in rice genetics, structural and functional genomics, comparative genomics, molecular biology and physiology, molecular breeding and comparative biology. Rice welcomes review articles and original papers in all of the aforementioned areas and serves as the primary source of newly published information for researchers and students in rice and related research.
期刊最新文献
The Rice Online Expression Profiles Array Database Version 2 (ROADv2): An Interactive Atlas for Rice Functional Genomics. Genetic Analysis and Fine Mapping of QTLs for Stigma Exsertion Rate in Rice. How Rice Responds to Temperature Changes and Defeats Heat Stress. Grain Quality of Panicle Portions in Chalky and Low-Chalky Rice Cultivars. Identification of the Cold-Related Genes COLD11 and OsCTS11 via BSA-seq and Fine Mapping at the Rice Seedling Stage.
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