ArticlePloS one2014
Discovering functional modules across diverse maize transcriptomes using COB, the Co-expression Browser.
Article in PloS one, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 15 papers, 1 of them a synthesis that pooled it.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
15 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Meta-analysis of drought-tolerant genotypes in Oryza sativa: A network-based approach.PloS one · 2019Pooled it
- The Importance of Regulatory Network Structure for Complex Trait Heritability and Evolution.Molecular biology and evolution · 2025Article
- Co-expression pan-network reveals genes involved in complex traits within maize pan-genome.BMC plant biology · 2022Article
- Identification of nodulation-related genes inPlant direct · 2020Article
- Genetic dissection of the gene coexpression network underlying photosynthesis in Populus.Plant biotechnology journal · 2020Article
- Trait ontology analysis based on association mapping studies bridges the gap between crop genomics and Phenomics.BMC genomics · 2019Article
- Recent advances in gene function prediction using context-specific coexpression networks in plants.F1000Research · 2019Review
- Integrating Coexpression Networks with GWAS to Prioritize Causal Genes in Maize.The Plant cell · 2018Article
- Construction and Optimization of a Large Gene Coexpression Network in Maize Using RNA-Seq Data.Plant physiology · 2017Article
- Differentially Regulated Orthologs in Sorghum and the Subgenomes of Maize.The Plant cell · 2017Article
- Co-expression network analysis of duplicate genes in maize (Zea mays L.) reveals no subgenome bias.BMC genomics · 2016Article
- A Network Approach of Gene Co-expression in theFrontiers in genetics · 2016Article
- Analysis of the Prefoldin Gene Family in 14 Plant Species.Frontiers in plant science · 2016Article
- Inference of Longevity-Related Genes from a Robust Coexpression Network of Seed Maturation Identifies Regulators Linking Seed Storability to Biotic Defense-Related Pathways.The Plant cell · 2015Article
- Correction: Discovering functional modules across diverse maize transcriptomes using COB, the co-expression browser.PloS one · 2015Article
Corrections and comments
- Erratum issued
Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Tools that provide improved ability to relate genotype to phenotype have the potential to accelerate breeding for desired traits and to improve our understanding of the molecular variants that underlie phenotypes. The availability of large-scale gene expression profiles in maize provides an opportunity to advance our understanding of complex traits in this agronomically important species. We built co-expression networks based on genome-wide expression data from a variety of maize accessions as well as an atlas of different tissues and developmental stages. We demonstrate that these networks reveal clusters of genes that are enriched for known biological function and contain extensive structure which has yet to be characterized. Furthermore, we found that co-expression networks derived from developmental or tissue atlases as compared to expression variation across diverse accessions capture unique functions. To provide convenient access to these networks, we developed a public, web-based Co-expression Browser (COB), which enables interactive queries of the genome-wide networks. We illustrate the utility of this system through two specific use cases: one in which gene-centric queries are used to provide functional context for previously characterized metabolic pathways, and a second where lists of genes produced by mapping studies are further resolved and validated using co-expression networks.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.