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

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. With the recent accumulation of RNA-seq data sets, the construction of RNA-seq-based GCNs has now become possible. Cereal crops, such as Hordeum vulgare (barley) and Sorghum bicolor (sorghum), are among the most important plants to humanity and contribute significantly to our food supply. However, co-expression network tools for these plants are outdated or lacking. In this study, we constructed global GCNs for barley and sorghum using 500 and 774 RNA-seq data sets, respectively. In addition, we curated the meta-information of these RNA-seq data sets and categorized them into four main tissue types, leaf, root, shoot, and flower/seed, and built tissue-specific GCNs. To enable GCN searching and visualization, we implemented a website and database named PlantNexus, offering an immersive environment for the exploration and visualization of gene expressions and co-expressions of barley and sorghum at the global and tissue-specific levels. PlantNexus is freely available at https://plantnexus.ohio.edu/.