PlantNexus: A Gene Co-expression Network Database and Visualization Tool for Barley and Sorghum

Yadi Zhou; Abhijit Sukul; John W Mishler-Elmore; Ahmed Faik; Michael A Held

doi:10.1093/pcp/pcac007

PlantNexus: A Gene Co-expression Network Database and Visualization Tool for Barley and Sorghum

Plant Cell Physiol. 2022 Apr 19;63(4):565-572. doi: 10.1093/pcp/pcac007.

Authors

Yadi Zhou¹, Abhijit Sukul¹, John W Mishler-Elmore¹, Ahmed Faik^{2

3}, Michael A Held^{1

3}

Affiliations

¹ Department of Chemistry and Biochemistry, Ohio University, Athens, OH 45701, USA.
² Department of Environmental and Plant Biology, Ohio University, Athens, OH 45701, USA.
³ Molecular and Cellular Biology Program, Ohio University, Athens, OH 45701, USA.

Abstract

Global gene co-expression networks (GCNs) are powerful tools for functional genomics whereby putative functions and regulatory mechanisms can be inferred by gene co-expression. Cereal crops, such as Hordeum vulgare (barley) and Sorghum bicolor (sorghum), are among the most important plants to civilization. However, co-expression network tools for these plants are lacking. Here, we have constructed global GCNs for barley and sorghum using existing RNA-seq data sets. Meta-information was manually curated and categorized by tissue type to also build tissue-specific GCNs. To enable GCN searching and visualization, we implemented a website and database named PlantNexus. PlantNexus is freely available at https://plantnexus.ohio.edu/.

Keywords: Barley; Database; Gene co-expression; RNA-seq; Sorghum; Transcriptomics.

MeSH terms

Edible Grain / genetics
Gene Regulatory Networks
Genomics
Hordeum* / genetics
Sorghum* / genetics

Abstract

MeSH terms

Grants and funding