WormBase as an integrated platform for the C. elegans ORFeome

Abstract

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.

Figure 1

Gene summary page for F10D2.4 (str-112). The gene summary page summarizes key information and serves as a gateway to related information. It is divided into multiple sections with links at the top of the table. Pages with ORFeome data, the Genome Browser page, the OST sequence page, and the PCR primer page all have links embedded in the gene summary page.

Figure 2

Sequence page for ORFeome sequence tags. The sequence summary page for OSTs contains a description about the OSTs, a graphical representation of the OSTs in the context of the genome, corresponding gene models, and the nucleotide sequence of the OSTs.

Figure 3

BLAST hits displayed in the genome browser. The BLAST/BLAT page displays links to the genome browser with the BLAST results shown in relation to the gene models and other corresponding features including the OSTs. This figure shows the genome browser view of BLAST hits with odr-10 as query against the C. elegans genome. The `BlastHSPs_from_Query' track shows the BLAST hits. Other tracks shown include Gene Models, ORFeome project Primers, and ORFeome sequence tags (best).