Online Access to C elegans Biology

The "worm community" is well-known for its open sharing of data and reagents. As noted earlier, numerous reagents including mutant and transgenic worm strains, cosmid, and yeast artificial chromosome clones, and expressed sequence tags (EST) clones are freely available from public resources (see Table 1). In addition, an extraordinary wealth of data on C. elegans is available online. Indeed, the worm community was an early pioneer in the use of the Internet for electronic data sharing. WormBase (http://www.wormbase.org/) is a particularly noteworthy database. It provides an exhaustive catalog of worm biology including identification of all known and predicted worm genes. Gene descriptions include genome location, mutant and RNAi phenotypes, expression patterns, microarray data, gene ontology, mutant alleles, and BLAST matches.

Table 1

Publicly Available Online C. elegans Databases and Resources

Site

Information and services available

Anatomy

• The Center for C. elegans Anatomy

Genomics

• ORFeome project Gene knockout

• The C. elegans Gene Knockout Consortium

• Japanese National Bioresource Project

Protein-protein interactions

• Vidal lab INTERACTome Project

Aid and train investigators in C. elegans electron microscopy

Online database of worm anatomy, anatomical methods, and cell function and identification

Online database of C. elegans electron microgaphs http://www.wormimage.org/ and associated data

http://www.aecom.yu.edu/wormem/ http://www.wormatlas.org/

Repository of information on genetics, genomics, and biology of C. elegans including gene sequence, gene expression patterns, RNA phenotypes, genetic maps, and worm anatomy Database of C. elegans ORFs

Produce null alleles of all known C. elegans genes; knockout animals available through the Caenorhabditis genetics center

Produce null alleles of all known C. elegans genes; provide knockout animals to investigators

Genome-scale protein-protein interaction mapping

http://www.wormbase.org/

http://worfdb.dfci.harvard.edu/

http://elegans.bcgsc.bc.ca/knockout.shtml

http://shigen.lab.nig.ac.jp/c.elegans/index.jsp

http://vidal.dfci.harvard.edu/main_pages/ interactome.htm

Gene expression patterns

• C. elegans Gene Expression Consortium

• The Hope Laboratory Expression Pattern Database

Worm reagents"

• Caenorhabditis Genetics Center

• MRC geneservice

• Open biosystems

• Sanger Institute

Miscellaneous

• Caenorhabditis elegans WWW Server

• Textpresso

• A Caenorhabditis elegans Survival Kit

Microarray, SAGE, and GFP analysis of gene expression paterns lacZ and GFP reporter expression database

Collect, maintain, and distribute worm strains; maintain a C. elegans bibliography Genome-wide RNAi library ORF clones

Fire Lab C. elegans Vector Kit: contains 288 vectors for lacZ and/or GFP expression, RNAi feeding, tagging C. elegans exons and introns with GFP, RNAi hairpin sequences, etc. ORF clones RNAi clones Provide cosmid and YAC clones to investigators

Links to many useful sites including an online catalog of methods

Search engine for C. elegans literature Online reviews of C. elegans biology and methodology

Links to many useful sites

http://elegans.bcgsc.ca/home/ge_consortium. html /

http://129.11.204.86:591/default.htm

http://biosci.umn.edu/CGC/CGChomepage. htm

http://www.geneservice.co.uk/products/ home/

http://www.addgene.org/pgvec1?f=c&cmd= showcol&colid=1

http://www.openbiosystems.com/index.php http://www.sanger.ac.uk/Projects/C_elegans/

http://elegans.swmed.edu/

http://www.wormimage.org/ http://www.wormbook.org/

http://members.tripod.com/C.elegans/ c_elegans_Introduction_Value_to_Biology Medicine.htm

" Check WormBase for latest information on ordering genomic clones.

GFP, green fluorescent protein; MRC, Medical Research Council; ORF, open reading frame; SAGE, serial analysis of gene expression; YAC, yeast artificial chromosome.

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