Bae Soon Hyung, Noh Yoo-Sun, Seo Pil Joon
Department of Chemistry, Seoul National University, Seoul 08826, South Korea.
School of Biological Sciences, Seoul National University, Seoul 08826, South Korea.
Comput Struct Biotechnol J. 2022 Jun 16;20:3234-3247. doi: 10.1016/j.csbj.2022.06.033. eCollection 2022.
In plants, differentiated somatic cells exhibit an exceptional ability to regenerate new tissues, organs, or whole plants. Recent studies have unveiled core genetic components and pathways underlying cellular reprogramming and tissue regeneration in plants. Although high-throughput analyses have led to key discoveries in plant regeneration, a comprehensive organization of large-scale data is needed to further enhance our understanding of plant regeneration. Here, we collected all currently available transcriptome datasets related to wounding responses, callus formation, organogenesis, somatic embryogenesis, and protoplast regeneration to construct REGENOMICS, a web-based application for plant REGENeration-associated transcriptOMICS analyses. REGENOMICS supports single- and multi-query analyses of plant regeneration-related gene-expression dynamics, co-expression networks, gene-regulatory networks, and single-cell expression profiles. Furthermore, it enables user-friendly transcriptome-level analysis of REGENOMICS-deposited and user-submitted RNA-seq datasets. Overall, we demonstrate that REGENOMICS can serve as a key hub of plant regeneration transcriptome analysis and greatly enhance our understanding on gene-expression networks, new molecular interactions, and the crosstalk between genetic pathways underlying each mode of plant regeneration. The REGENOMICS web-based application is available at http://plantregeneration.snu.ac.kr.
在植物中，分化的体细胞展现出再生新组织、器官或完整植株的非凡能力。最近的研究揭示了植物细胞重编程和组织再生的核心遗传成分及途径。尽管高通量分析已在植物再生领域取得了关键发现，但仍需要对大规模数据进行全面整合，以进一步加深我们对植物再生的理解。在此，我们收集了所有目前可用的与伤口应答、愈伤组织形成、器官发生、体细胞胚胎发生和原生质体再生相关的转录组数据集，构建了REGENOMICS，这是一个基于网络的用于植物再生相关转录组学分析的应用程序。REGENOMICS支持对植物再生相关基因表达动态、共表达网络、基因调控网络和单细胞表达谱进行单查询和多查询分析。此外，它还能对REGENOMICS存储的以及用户提交的RNA测序数据集进行用户友好型的转录组水平分析。总体而言，我们证明REGENOMICS可作为植物再生转录组分析的关键枢纽，并极大地增进我们对基因表达网络、新的分子相互作用以及植物再生各模式潜在遗传途径之间相互作用的理解。基于网络的REGENOMICS应用程序可在http://plantregeneration.snu.ac.kr获取。
