ArticleThe Plant cell2021
Co-expression networks in Chlamydomonas reveal significant rhythmicity in batch cultures and empower gene function discovery.
Article in The Plant cell, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed.
- The Role of Myeloperoxidase in Osteoarthritis and Its Potential Modulation by Resveratrol: An Integrated Study.FASEB journal : official publication of the Federation of American Societies for Experimental Biology · 2026Article
- A kingdom-wide full-length RNA atlas reveals the evolutionary landscapes of plant poly(A) tails.Genome biology · 2026Article
- Integrating co-expression network analysis and machine learning to reveal the regulatory landscape ofPeerJ · 2026Article
- Identification and validation of tricarboxylic acid cycle-related diagnostic biomarkers for diabetic nephropathy via weighted gene co-expression network analysis and single-cell transcriptome analysis.Acta diabetologica · 2025Article
- Identification of Biomarkers and Mechanisms Associated with Apoptosis in Recurrent Pregnancy Loss.Biochemical genetics · 2025Article
- Pangenome analysis of transposable element insertion polymorphisms reveals features underlying cold tolerance in rice.Nature communications · 2025Article
- Identification of immune-associated biomarkers in diagnosing allergic rhinitis.The World Allergy Organization journal · 2025Article
- Too dim, too bright, and just right: Systems analysis of the Chlamydomonas diurnal program under limiting and excess light.The Plant cell · 2025Article
- Immunophenotyping identifies key immune biomarkers for coronary artery disease through machine learning.PloS one · 2025Article
- Review
- Iron rescues glucose-mediated photosynthesis repression during lipid accumulation in the green alga Chromochloris zofingiensis.Nature communications · 2024Article
- Pyroptosis-Related Genes as Diagnostic Markers in Chronic Obstructive Pulmonary Disease and Its Correlation with Immune Infiltration.International journal of chronic obstructive pulmonary disease · 2024Article
- Fungal co-expression network analyses identify pathogen gene modules associated with host insect invasion.Microbiology spectrum · 2023Article
- Chlamydomonas reinhardtii: a model for photosynthesis and so much more.Nature methods · 2023Article
- Identification of biomarkers and immune infiltration in acute myocardial infarction and heart failure by integrated analysis.Bioscience reports · 2023Article
- Zeaxanthin epoxidase is involved in the carotenoid biosynthesis and light-dependent growth of the marine alga Nannochloropsis oceanica.Biotechnology for biofuels and bioproducts · 2023Article
- ARHGAP11A Is a Novel Prognostic and Predictive Biomarker Correlated with Immunosuppressive Microenvironment in Clear Cell Renal Cell Carcinoma.International journal of molecular sciences · 2023Article
- A potential EARLY FLOWERING 3 homolog in Chlamydomonas is involved in the red/violet and blue light signaling pathways for the degradation of RHYTHM OF CHLOROPLAST 15.PLoS genetics · 2022Article
- The landscape of Chlamydomonas histone H3 lysine 4 methylation reveals both constant features and dynamic changes during the diurnal cycle.The Plant journal : for cell and molecular biology · 2022Article
- Systematic characterization of gene function in the photosynthetic alga Chlamydomonas reinhardtii.Nature genetics · 2022Article
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2 authors.
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Abstract
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 of our method. Surprisingly, Chlamydomonas experiments retained a significant rhythmic component across the transcriptome, suggesting an underappreciated variable during sample collection, even in samples collected in constant light. Our results therefore document substantial residual synchronization in batch cultures, contrary to assumptions of asynchrony. We provide step-by-step protocols for the analysis of co-expression across transcriptome data sets from Chlamydomonas and other species to help foster gene function discovery.
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