WormBase as an integrated platform for the C. elegans ORFeome.
The ORFeome project has validated and corrected a large number of predicted gene models in the nematode C. elegans, and has provided an enormous resource for proteome-scale studies. To make the resource useful to the research and teaching community, it needs to be integrated with other large-scale data sets, including the C. elegans genome, cell lineage, neurological wiring diagram, transcriptome, and gene expression map. This integration is also critical because the ORFeome data sets, like other 'omics' data sets, have significant false-positive and false-negative rates, and comparison to related data is necessary to make confidence judgments in any given data point. WormBase, the central data repository for information about C. elegans and related nematodes, provides such a platform for integration. In this report, we will describe how C. elegans ORFeome data are deposited in the database, how they are used to correct gene models, how they are integrated and displayed in the context of other data sets at the WormBase Web site, and how WormBase establishes connection with the reagent-based resources at the ORFeome project Web site.
Chen
Nansheng
N
Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA. chenn@cshl.org
Lawson
Daniel
D
Bradnam
Keith
K
Harris
Todd W
TW
Stein
Lincoln D
LD
D000818:Animals; D001483:Base Sequence; D017173:Caenorhabditis elegans / Q000235:genetics*; D029742:Caenorhabditis elegans Proteins / Q000235:genetics* / Q000378:metabolism; D019295:Computational Biology; D030541:Databases, Genetic; D017238:Genes, Helminth / Q000502:physiology*; D023281:Genomics; D016247:Information Storage and Retrieval; D008969:Molecular Sequence Data; D016366:Open Reading Frames / Q000235:genetics*; D020543:Proteome; D040901:Proteomics
D029742:Caenorhabditis elegans Proteins; D020543:Proteome