Co-expression networks in Chlamydomonas reveal significant rhythmicity in batch cultures and empower gene function discovery

The unicellular green alga Chlamydomonas reinhardtii is a choice reference system for the study of photosynthesis and chloroplast metabolism, cilium assembly and function, lipid and starch metabolism, and metal homeostasis. Despite decades of research, the functions of thousands of genes remain largely unknown, and new approaches are needed to categorically assign genes to cellular pathways. Growing collections of transcriptome and proteome data now allow a systematic approach based on integrative co-expression analysis. We used a dataset comprising 518 deep transcriptome samples derived from 58 independent experiments to identify potential co-expression relationships between genes. We visualized co-expression potential with the R package corrplot, to easily assess co-expression and anti-correlation between genes. We extracted several hundred high-confidence genes at the intersection of multiple curated lists involved in cilia, cell division, and photosynthesis, illustrating the power o...单细胞绿藻莱茵衣藻（Chlamydomonas reinhardtii）是研究光合作用与叶绿体代谢、纤毛组装与功能、脂质与淀粉代谢以及金属稳态的优选参考模式系统。尽管已有数十年的研究积累，仍有数以千计的基因功能尚未明确，亟需开发全新方法以将基因精准归类至各类细胞通路中。日益丰富的转录组与蛋白质组数据资源，为基于整合共表达分析的系统性研究提供了可行支撑。本研究采用包含58项独立实验所得的518份深度转录组样本的数据集，以鉴定基因间潜在的共表达关联。我们借助R语言corrplot工具包对共表达潜力进行可视化处理，可便捷评估基因间的共表达与抗相关关系。我们从多个经人工整理的、涉及纤毛、细胞分裂及光合作用的基因列表的交集区域中，筛选出了数百个高置信度基因，这充分彰显了该研究方法的应用潜力……