The complex cellular network was formed by the interacting gene modules. Building the high-quality RNA-seq-based Gene Co-expression Network (GCN) is critical for uncovering these modules and understanding the phenotypes of an organism. Here, we established and analyzed the RNA-seq-based GCNs in two monocot species rice and maize, and two eudicot species Arabidopsis and soybean, and subdivided them into co-expressed modules. Taking rice as an example, we associated these modules with biological functions and agronomic traits by enrichment analysis, and discovered a large number of conditin-specific or tissue-specific modules. In addition, we also explored the regulatory mechanism of the modules by enrichment of the known cis-elements, transcription factors and miRNA targets. Their coherent enrichment with the inferred functions of the modules revealed their synergistic effect on the gene expression regulation. Moreover, the comparative analysis of gene co-expression was performed to identify conserved and species-specific functional modules across 4 plant species. We discovered that the modules shared across 4 plants participate in the basic biological processes, whereas the species-specific modules were involved in the spatiotemporal-specific processes linking the genotypes to phenotypes. Our research provides the massive modules relating to the cellular activities and agronomic traits in several model and crop plant species.
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