biostudies-literatureUnknown24(6)Piya SGene co-expression network analysis is an efficient systems biology approach for the discovery of novel gene functions and trait-associated gene modules. To identify clusters of functionally related genes involved in soybean nodule formation and development, we performed a weighted gene co-expression network analysis. Two nodule-specific modules (NSM-1 and NSM-2, containing 304 and 203 genes, respectively) were identified. The NSM-1 gene promoters were significantly enriched in cis-binding elements for ERF, MYB, and C2H2-type zinc transcription factors, whereas NSM-2 gene promoters were enriched in cis-binding elements for TCP, bZIP, and bHLH transcription factors, suggesting a role of these regulatory factors in the transcriptional activation of nodule co-expressed genes. The co-expressedMolecular plant pathology628-636https://www.ebi.ac.uk/biostudies/studies/S-EPMC10189762biostudies-literatureSoybean gene co-expression network analysis identifies two co-regulated gene modules associated with nodule formation and development.PMC10189762Lakhssassi NZadegan SBKrishnan HBPiya SPantalone VMeksem KKnizia DHewezi TShipp SfalseSoybean gene co-expression network analysis identifies two co-regulated gene modules associated with nodule formation and development.Gene co-expression network analysis is an efficient systems biology approach for the discovery of novel gene functions and trait-associated gene modules. To identify clusters of functionally related genes involved in soybean nodule formation and development, we performed a weighted gene co-expression network analysis. Two nodule-specific modules (NSM-1 and NSM-2, containing 304 and 203 genes, respectively) were identified. The NSM-1 gene promoters were significantly enriched in cis-binding elements for ERF, MYB, and C2H2-type zinc transcription factors, whereas NSM-2 gene promoters were enriched in cis-binding elements for TCP, bZIP, and bHLH transcription factors, suggesting a role of these regulatory factors in the transcriptional activation of nodule co-expressed genes. The co-expressed2023-01-01T00:00:00Z2023 Jun2025-04-05T16:14:21.608Z2025-04-05T16:14:21.608ZS-EPMC101897623697502410.1111/mpp.13327