title: Genome-wide modeling of complex phenotypes in Caenorhabditis elegans and Drosophila melanogaster.
abstract: BACKGROUND
  The genetic and molecular basis for many intermediate and end stage phenotypes in model systems such as C. elegans and D. melanogaster has long been known to involve pleiotropic effects and complex multigenic interactions. Gene sets are groups of genes that contribute to multiple biological or molecular phenomena. They have been used in the analysis of large molecular datasets such as microarray data, Next Generation sequencing, and other genomic datasets to reveal pleiotropic and multigenic contributions to phenotypic outcomes. Many model systems lack species specific organized phenotype based gene sets to enable high throughput analysis of large molecular datasets.
  
  
  CONCLUSIONS
  Here, we describe two novel collections of gene sets in C. elegans and D. melanogaster that are based exclusively on genetically determined phenotypes and use a controlled phenotypic ontology. We use these collections to build genome-wide models of thousands of defined phenotypes in both model species. In addition, we demonstrate the utility of these gene sets in systems analysis and in analysis of gene expression-based molecular datasets and show how they are useful in analysis of genomic datasets connecting multigenic gene inputs to complex phenotypes.
  
  
  CONCLUSIONS
  Phenotypic based gene sets in both C. elegans and D. melanogaster are developed, characterized, and shown to be useful in the analysis of large scale species-specific genomic datasets. These phenotypic gene set collections will contribute to the understanding of complex phenotypic outcomes in these model systems.
authors.affiliation: Gene Expression and Genomics Unit, Laboratory of Genetics, National Institute on Aging, National Institutes of Health, Biomedical Research Center, 251 Bayview Boulevard, Baltimore, MD 21224, USA. beckerk@grc.nia.nih.gov.
authors.forename: Supriyo
authors.initials: S
authors.lastname: De
authors.forename: Yongqing
authors.initials: Y
authors.lastname: Zhang
authors.forename: Catherine A
authors.initials: CA
authors.lastname: Wolkow
authors.forename: Sige
authors.initials: S
authors.lastname: Zou
authors.forename: Ilya
authors.initials: I
authors.lastname: Goldberg
authors.forename: Kevin G
authors.initials: KG
authors.lastname: Becker
mesh_terms: D000818:Animals; D017173:Caenorhabditis elegans / Q000235:genetics* / Q000378:metabolism; D030541:Databases, Genetic; D004331:Drosophila melanogaster / Q000235:genetics* / Q000378:metabolism; D063990:Gene Ontology; D017238:Genes, Helminth; D017344:Genes, Insect; D058685:Genetic Pleiotropy; D016678:Genome; D008957:Models, Genetic; D020411:Oligonucleotide Array Sequence Analysis; D010641:Phenotype; D025341:Principal Component Analysis; D059467:Transcriptome