Systematic analysis of RNA-seq-based gene co-expression

The complex cellular network was formed by the interacting gene modules. Building 10 the high-quality RNA-seq-based Gene Co-expression Network (GCN) is critical for 11 uncovering these modules and understanding the phenotypes of an organism. Here, 12 we established and analyzed the RNA-seq-based GCNs in two monocot species rice 13 and maize, and two eudicot species Arabidopsis and soybean, and subdivided them 14 into co-expressed modules. Taking rice as an example, we associated these modules 15 with biological functions and agronomic traits by enrichment analysis, and discovered 16 a large number of conditin-specific or tissue-specific modules. In addition, we also 17 explored the regulatory mechanism of the modules by enrichment of the known 18 cis-elements, transcription factors and miRNA targets. Their coherent enrichment with 19 the inferred functions of the modules revealed their synergistic effect on the gene 20 expression regulation. Moreover, the comparative analysis of gene co-expression was 21 performed to identify conserved and species-specific functional modules across 4 22 plant species. We discovered that the modules shared across 4 plants participate in the 23 basic biological processes, whereas the species-specific modules were involved in the 24 spatiotemporal-specific processes linking the genotypes to phenotypes. Our research 25 provides the massive modules relating to the cellular activities and agronomic traits in 26 several model and crop plant species. 27