Several public databases, such as GEO, ArrayExpress and ENA (, accessed on 10 March 2022), have allowed researchers to upload transcriptomic data, enabling data reproducibility for others. Innovations in microarray technologies, high-throughput RNA sequencing (RNA-seq) platforms and computational biology have facilitated large-scale studies on gene expression and have led to the accumulation of transcriptomic data. The expression patterns of a gene across different tissues, development stages and conditions provide insights into when and where a gene is required, as well as clues for the gene’s function. In plant sciences, transcriptomics is increasingly being used to understand the expression patterns in different tissues and conditions, and to unravel the molecular mechanisms controlling biological processes. Transcriptomics is the measurement of transcript expression levels in different tissues, stages or conditions. With this effort, the researcher would be able to explore and utilise gene co-expression network databases for crops improvement. The highlights of gene co-expression network databases and the tools presented here will pave the way for a robust interpretation of biologically relevant information. This review presents the features and the most recent gene co-expression network databases in crops and summarises the present status of the tools that are widely used for constructing the gene co-expression network. Although these resources remain scattered across the Internet, such databases complement each other and support efficient growth in the functional genomics area. To date, several gene co-expression network databases that store correlation values, expression profiles, gene names and gene descriptions have been developed. The generated transcriptomics data can be utilised to produce a gene co-expression network that is one of the essential downstream omics data analyses. Transcriptomics has significantly grown as a functional genomics tool for understanding the expression of biological systems.
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