ArticleProceedings of the National Academy of Sciences of the United States of America2019
Comparative transcriptomics method to infer gene coexpression networks and its applications to maize and rice leaf transcriptomes.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 63 papers.
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63 citing papers in PubMed, 134 citations in OpenAlex.
- Profiling maize embryonic leaf development and discovering new genes using high-resolution spatial long-read isoform sequencing.Nature plants · 2026Article
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- Salt priming coordinates transcriptional and epigenetic states for enhanced salt tolerance in mung bean (Vigna radiata).Communications biology · 2026Article
- Integrated WGCNA and TO-GCN analysis reveals pathways and genes underlying salt tolerance in Sesbania cannabina.BMC plant biology · 2026Article
- Lipid metabolism-driven regulatory networks involved in cone senescence and seed maturation in pine (Pinus massoniana).Communications biology · 2026Article
- Serial Spatial Transcriptomes Reveal Regulatory Transitions in Maize Leaf Development.Plant biotechnology journal · 2026Article
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- Integrative multi-omics analysis reveals the genetic architecture of floral traits inHorticulture research · 2026Article
- Genome and transcriptomics provide insights on stipular spine morphogenesis inForestry research · 2026Article
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- GWAS and multi-omics study reveal OsJAR2 associated jasmonate biosynthesis contributes to Southern rice black-streaked dwarf virus resistance in rice.BMC genomics · 2025Article
- Dose-dependent transcriptional reprogramming and lipid-associated defense under salt stress in mung bean (Vigna radiata).BMC plant biology · 2025Article
- Growth-limiting drought increases sensitivity of Asian rice (Oryza sativa) leaves to heat shock through physiological and spatially distinct transcriptomic responses.The Plant journal : for cell and molecular biology · 2025Article
- Comparative Transcriptome Reveals Conserved Gene Expression in Reproductive Organs in Solanaceae.International journal of molecular sciences · 2025Article
- Molecular mechanism of response to low-temperature during the natural overwintering period of Rosa persica.Plant cell reports · 2025Article
- Genome-wide analysis of the TCP transcription factor family in mung bean and its dynamic regulatory network under salt stress.Frontiers in plant science · 2025Article
- Time-Course Transcriptome Analysis Reveals Distinct Transcriptional Regulatory Networks in Resistant and Susceptible Grapevine Genotypes in Response to White Rot.International journal of molecular sciences · 2024Article
- Multi-omics analyzes of Rosa gigantea illuminate tea scent biosynthesis and release mechanisms.Nature communications · 2024Article
- Haplotype-resolved chromosomal-level genome assembly reveals regulatory variations in mulberry fruit anthocyanin content.Horticulture research · 2024Article
3 more citing papers are in PubMed but not listed here.
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Authors and funding
15 authors at 6 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Time-series transcriptomes of a biological process obtained under different conditions are useful for identifying the regulators of the process and their regulatory networks. However, such data are 3D (gene expression, time, and condition), and there is currently no method that can deal with their full complexity. Here, we developed a method that avoids time-point alignment and normalization between conditions. We applied it to analyze time-series transcriptomes of developing maize leaves under light-dark cycles and under total darkness and obtained eight time-ordered gene coexpression networks (TO-GCNs), which can be used to predict upstream regulators of any genes in the GCNs. One of the eight TO-GCNs is light-independent and likely includes all genes involved in the development of Kranz anatomy, which is a structure crucial for the high efficiency of photosynthesis in C
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