PEO: Plant Expression Omnibus – a comparative transcriptomic database for 103 Archaeplastida

SUMMARY The Plant Expression Omnibus (PEO) is a web application that provides biologists with access to gene expression insights across over 100 plant species, ~60 000 manually annotated RNA‐seq samples, and more than 4 million genes. The tool allows users to explore the expression patterns of genes...

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Bibliographic Details
Published in:The Plant journal : for cell and molecular biology 2024-03, Vol.117 (5), p.1592-1603
Main Authors: Koh, Eugene, Goh, William, Julca, Irene, Villanueva, Erielle, Mutwil, Marek
Format: Article
Language:English
Subjects:
Annotations
Applications programs
Arabidopsis - genetics
Biosynthesis
Capsaicin
coexpression
comparative
Databases, Factual
Gene expression
Gene Expression Profiling
Gene Expression Regulation, Plant - genetics
gene families
Genes
pathway
Peppers
Plant species
Plants (botany)
Plants - genetics
Plants - metabolism
Pollen
RNA-Seq
RNA‐sequencing
Transcriptome - genetics
Transcriptomics
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Description
Summary:SUMMARY The Plant Expression Omnibus (PEO) is a web application that provides biologists with access to gene expression insights across over 100 plant species, ~60 000 manually annotated RNA‐seq samples, and more than 4 million genes. The tool allows users to explore the expression patterns of genes across different organs, identify organ‐specific genes, and discover top co‐expressed genes for any gene of interest. PEO also provides functional annotations for each gene, allowing for the identification of genetic modules and pathways. PEO is designed to facilitate comparative kingdom‐wide gene expression analysis and provide a valuable resource for plant biology research. We provide two case studies to demonstrate the utility of PEO in identifying candidate genes in pollen coat biosynthesis in Arabidopsis and investigating the biosynthetic pathway components of capsaicin in Capsicum annuum. The database is freely available at https://expression.plant.tools/. Significance Statement Plant Expression Omnibus is an online database that contains expression data for more than 4 million genes belonging to 103 species in Archaeplastida. The database offers expression profile viewers, co‐expression analyses, organ‐specific expression, and more.
ISSN:0960-7412
1365-313X
DOI:10.1111/tpj.16566