Previously we implemented a simple web-based database interface for genome-scale data mining at the protein (rather than the DNA) level for experimental planning - hosted at: http://genome.sfu.ca/gexplore/. The interface allows individual or combinatorial searches for proteins with certain domains, expression in particular tissues or specific phenotypes. Genes in a given interval can be retrieved for vetting candidate genes in positional mapping experiments. The database, which contains also GO terms and homology information, has been updated regularly using Wormbase data. Recently new datasets including stage- and sex-specific RNAseq expression data (see Gerstein et al., Science 330:1775-87) have been processed and added. We are currently preparing a major update of GExplore to include several novel features and datasets. We included protein domain data using Pfam and SMART annotations for all core species in Wormbase (C. elegans, C. briggsae, C. brenneri, C. japonica, C. remanei and P. pacificus). We extended the manually curated list of protein domains that can be searched by simple abbreviations, e.g. 'IG' to retrieve all proteins containing Pfam or SMART domains referring to ImmunoGlobulin domains, to over 450 domains. Proteins containing a particular Pfam or SMART domain can be identified using Pfam or SMART identifiers. In addition to a graphic display of the domain organization of proteins, the protein sequences are available for display and download. A new interface allows users to observe where mutations are located within a protein of interest. The output can be limited to mutations affecting certain protein domains. Our database contains mutations accessible through Wormmart and will be updated as more recent Wormbase data will become available for general data mining. The database also includes mutations isolated by the Million Mutation Project, which have been released recently by the Moerman and Waterston labs (Thompson et al. submitted). Independently of GExplore we maintain a web-based interface to search for mutations from the Million Mutation Project (hosted at http://genome.sfu.ca/mmp/). We will present the current progress in updating the GExplore website and underlying database.

Affiliation:
- Biol Sci, Simon Fraser Univ, Burnaby, BC, Canada