title: Discovering functional modules across diverse maize transcriptomes using COB, the Co-expression Browser.
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.
authors.affiliation: Biomedical Informatics and Computational Biology Graduate Program, University of Minnesota Rochester, Rochester, Minnesota, United States of America.
authors.forename: Robert J
authors.initials: RJ
authors.lastname: Schaefer
authors.affiliation: Department of Computer Science and Engineering, University of Minnesota, Minneapolis, Minnesota, United States of America.
authors.forename: Roman
authors.initials: R
authors.lastname: Briskine
authors.affiliation: Microbial and Plant Genomics Institute, Department of Plant Biology, University of Minnesota, Saint Paul, Minnesota, United States of America.
authors.forename: Nathan M
authors.initials: NM
authors.lastname: Springer
authors.affiliation: Biomedical Informatics and Computational Biology Graduate Program, University of Minnesota Rochester, Rochester, Minnesota, United States of America; Department of Computer Science and Engineering, University of Minnesota, Minneapolis, Minnesota, United States of America.
authors.forename: Chad L
authors.initials: CL
authors.lastname: Myers
mesh_terms: D016000:Cluster Analysis; D018506:Gene Expression Regulation, Plant; D063990:Gene Ontology; D053263:Gene Regulatory Networks; D020407:Internet; D040641:Quantitative Trait Loci / Q000235:genetics; D059467:Transcriptome / Q000235:genetics*; D003313:Zea mays / Q000235:genetics*