C. elegans bioinformatics resources
Two primary websites
- Wormbase
- main data repository, CHECK HERE FIRST!!
- User’s
guide
- Caenorhabditis elegans WWW
Server
- links to everything! data, literature, researchers, protocols, newsgroup, job and meeting announcements
Does the worm have an ortholog of my gene?
Has this gene been studied?
- Worm
literature index
- published papers and meeting abstracts
Is there a mutant, and can I get it?
- Caenorhabditis
Genetics Center (CGC)
- Worm strain stock center
- Worm strain stock center
- Gene knockout consortiums (deletion mutants existing or in the pipeline)
What is the gene’s RNAi phenotype?
Are there genomic and cDNA clones, and can I get them?
- See Wormbase for clone info
- Genomic clones (cosmids, YACs)
- please send all requests to Audrey Fraser (aef@sanger.ac.uk) with a cc to Ratna Shownkeen (rs2@sanger.ac.uk); include a FedEx or DHL account number.
- cDNA “yk” clones
- please send all requests to Dr. Yuji Kohara (ykohara@pop.lab.nig.ac.jp)
- To purchase ORFeome clones (in Gateway vectors, made by Vidal lab)
What is the gene’s expression pattern?
- Nematode Expression Pattern Database (NEXTDB)
- in situ hybridization data, Kohara lab, Japan
- Hope lab Expession Pattern Database
- LacZ reporter stainings
- Microarray data
- Kim lab, Stanford
What does the protein bind to?
- Worm Interactome
- Yeast two hybrid data set, Vidal laboratory, Harvard