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

Plant Cell Physiol. 2022 Jan 12;pcac007. doi: 10.1093/pcp/pcac007. Online ahead of print.

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: RNA-seq; barley; database; gene co-expression; sorghum; transcriptomics.