WormBase: A comprehensive data resource for Caenorhabditis biology and genomics

Nucleic Acids Research

Volumn 33, Issue DATABASE ISS., 2005, Pages

  Chen, Nansheng ^e   Harris, Todd W ^e   Antoshechkin, Igor ^a   Bastiani, Carol ^a   Bieri, Tamberlyn ^b   Blasiar, Darin ^b   Bradnam, Keith ^c   Canaran, Payan ^e   Chan, Juancarlos ^a   Chen, Chao Kung ^c   Chen, Wen J ^a   Cunningham, Fiona ^e   Davis, Paul ^c   Kenny, Eimear ^a   Kishore, Ranjana ^a   Lawson, Daniel ^c   Lee, Raymond ^a   Muller, Hans Michael ^a   Nakamura, Cecilia ^a   Pai, Shraddha ^d   Ozersky, Philip ^b   Petcherski, Andrei ^a   Rogers, Anthony ^c   Sabo, Aniko ^b   Schwarz, Erich M ^a   Van Auken, Kimberly ^a   Wang, Qinghua ^a   Durbin, Richard ^c   Spieth, John ^b   Sternberg, Paul W ^a   Stein, Lincoln D ^e   more..

^a CALIFORNIA INSTITUTE OF TECHNOLOGY   (United States)

^b WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

^c WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^d WATSON SCHOOL OF BIOLOGICAL SCIENCES   (United States)

^e Watson School of Biological Sciences   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACCESS TO INFORMATION; ARTICLE; CAENORHABDITIS; CAENORHABDITIS ELEGANS; COMPUTER INTERFACE; EXPRESSED SEQUENCE TAG; GENBANK; GENE SEQUENCE; GENETIC CONSERVATION; GENETIC DATABASE; GENETIC MODEL; GENOMICS; HUMAN COMPUTER INTERACTION; INFORMATION PROCESSING; MEDICAL INFORMATION SYSTEM; MOLECULAR BIOLOGY; MOLECULAR PHYLOGENY; NEMATODE; NONHUMAN; ORTHOLOGY; PRIORITY JOURNAL; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; SEQUENCE ALIGNMENT; SERIAL ANALYSIS OF GENE EXPRESSION; SPECIES DIFFERENCE; WORMBASE; CONTROLLED STUDY; FACTUAL DATABASE; GENOME ANALYSIS; SEQUENCE ANALYSIS; STRUCTURE ANALYSIS; THREE DIMENSIONAL IMAGING;

ANIMALS; CAENORHABDITIS; CAENORHABDITIS ELEGANS; CAENORHABDITIS ELEGANS PROTEINS; DATABASES, GENETIC; GENE EXPRESSION PROFILING; GENOMICS; PROTEIN CONFORMATION; SOFTWARE; SYSTEMS INTEGRATION; TWO-HYBRID SYSTEM TECHNIQUES; USER-COMPUTER INTERFACE;

CAENORHABDITIS; CAENORHABDITIS ELEGANS; NEMATODA;

EID: 13444254287     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gki066     Document Type: Article

References (33)

1. Riddle,D.L., Blumenthal,T., Meyer,B.J. and Priess,J.R. (1997) C. elegans II. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
2. Harris,T.W., Chen,N., Cunningham,F., Tello-Ruiz,M., Antoshechkin,I., Bastiani,C., Bieri,T., Blasiar,D., Bradnam,K., Chan,J. et al. (2004) WormBase: a multi-species resource for nematode biology and genomics. Nucleic Acids Res., 32 (Database issue), D411-D417.
3. Harris,T.W., Lee,R., Schwarz,E., Bradnam,K., Lawson,D., Chen,W., Blasier,D., Kenny,E., Cunningham,F., Kishore,R. et al. (2003) WormBase: a cross-species database for comparative genomics. Nucleic Acids Res., 31, 133-137.
4. Stein,L., Sternberg,P., Durbin,R., Thierry-Mieg,J. and Spieth,J. (2001) WormBase: network access to the genome and biology of Caenorhabditis elegans. Nucleic Acids Res., 29, 82-86.
5. The C.elegans Sequencing Consortium (1998) Genome sequence of the nematode C.elegans: a platform for investigating biology. Science, 282, 2012-2018.
6. Chen,N., Lawson,D., Bradnam,K. and Harris,T.W. (2004) WormBase as an integrated platform for the C. elegans ORFeome. Genome Res. 14, 2155-2161.
7. Kamath,R.S., Fraser,A.G., Dong,Y., Poulin,G., Durbin,R., Gotta,M., Kanapin,A., Le Bot,N., Moreno,S., Sohrmann,M. et al. (2003) Systematic functional analysis of the Caenorhabditis elegans genome using RNAi. Nature, 421, 231-237.
8. Kim,S.K., Lund,J., Kiraly,M., Duke,K., Jiang,M., Stuart,J.M., Eizinger,A., Wylie,B.N. and Davidson,G.S. (2001) A gene expression map for Caenorhabditis elegans. Science, 293, 2087-2092.
9. Li,S., Armstrong,C.M., Bertin,N., Ge,H., Milstein,S., Boxem,M., Vidalain,P.O., Han,J.D., Chesneau,A., Hao,T. et al. (2004) A map of the interactome network of the metazoan C. elegans. Science, 303, 540-543.
10. Jones,S.J., Riddle,D.L., Pouzyrev,A.T., Velculescu,V.E., Hillier,L., Eddy,S.R., Stricklin,S.L., Baillie,D.L., Waterston,R. and Marra,M.A. (2001) Changes in gene expression associated with developmental arrest and longevity in Caenorhabditis elegans. Genome Res., 11, 1346-1352.
11. McKay,S.J., Johnsen,R., Khattra,J., Asano,J., Baillie,D.L., Chan,S., Dube,N., Fang,L., Goszczynski,B., Ha,E. et al. (2004) Cold Spring Harbor Symposia on Quantitative Biology. Cold Spring Harbor, NY, Vol. 68, pp. 159-170.
12. Stein,L.D., Bao,Z., Blasiar,D., Blumenthal,T., Brent,M.R., Chen,N., Chinwalla,A., Clarke,L., Clee,C., Coghlan,A. et al. (2003) The genome sequence of Caenorhabditis briggsae: a platform for comparative genomics. PLoS Biol., 1, E45.
13. Gupta,B.P. and Sternberg,P.W. (2003) The draft genome sequence of the nematode Caenorhabditis briggsae, a companion to C. elegans. Genome Biol., 4, 238.
14. Tatusov,R.L., Fedorova,N.D., Jackson,J.D., Jacobs,A.R., Kiryutin,B., Koonin,E.V., Krylov,D.M., Mazumder,R., Mekhedov,S.L., Nikolskaya,A.N. et al. (2003) The COG database: an updated version includes eukaryotes. BMC Bioinformatics, 4, 41.
15. Hwang,B.J., Muller,H.M. and Sternberg,P.W. (2004) Genome annotation by high-throughput 5′ RNA end determination. Proc. Natl Acad. Sci. USA, 101, 1650-1655.
16. Berman,H.M., Battistuz,T., Bhat,T.N., Bluhm,W.F., Bourne,P.E., Burkhardt,K., Feng,Z., Gilliland,G.L., Iype,L., Jain,S. et al. (2002) The Protein Data Bank. Acta Crystallogr. D Biol. Crystallogr., 58, 899-907.
17. Stajich,J.E., Block,D., Boulez,K., Brenner,S.E., Chervitz,S.A., Dagdigian,C., Fuellen,G., Gilbert,J.G., Korf,I., Lapp,H. et al. (2002) The Bioperl toolkit: Perl modules for the life sciences. Genome Res., 12, 1611-1618.
18. Dowell,R.D., Jokerst,R.M., Day,A., Eddy,S.R. and Stein,L. (2001) The distributed annotation system. BMC Bioinformatics, 2 7.
19. Stein,L.D. and Thierry-Mieg,J. (1998) Scriptable access to the Caenorhabditis elegans genome sequence and other ACEDB databases. Genome Res., 8, 1308-1315.
20. Lopez,R., Silventoinen,V., Robinson,S., Kibria,A. and Gish,W. (2003) WU-Blast2 server at the European Bioinformatics Institute. Nucleic Acids Res., 31, 3795-3798.
21. Kent,W.J. (2002) BLAT - the BLAST-like alignment tool. Genome Res., 12, 656-664.
22. Schuler,G.D. (1997) Sequence mapping by electronic PCR. Genome Res., 7, 541-550.
23. Muller,H.M., Kenny,E. and Sternberg,P. (2004) Testpresso: an ontology-based information retrieval and extraction system for C. elegans literature. PLoS Biol., 2, e309.
24. Bigelow,H.R., Wenick,A.S., Wong,A. and Hobert,O. (2004) CisOrtho: a program pipeline for genome-wide identification of transcription factor target genes using phylogenetic footprinting. BMC Bioinformatics, 5, 27.
25. Lewis,S.E., Searle,S.M., Harris,N., Gibson,M., Lyer,V., Richter,J., Wiel,C., Bayraktaroglir,L., Birney,E., Crosby,M.A. et al. (2002) Apollo: a sequence annotation editor. Genome Biol., 3 RESEARCH0082.
26. Stein,L.D., Mungall,C., Shu,S., Caudy,M., Mangone,M., Day,A., Nickerson,E., Stajich,J.E., Harris,T.W., Arva,A. et al. (2002) The generic genome browser: a building block for a model organism system database. Genome Res., 12, 1599-1610.
27. FlyBase (2003) The FlyBase database of the Drosophila genome projects and community literature. Nucleic Acids Res., 31 172-175.
28. Christie,K.R., Weng,S., Balakrishnan,R., Costanzo,M.C., Dolinski,K., Dwight,S.S., Engel,S.R., Feierbach,B., Fisk,D.G., Hirschman,J.E. et al. (2004) Saccharomyces Genome Database (SGD) provides tools to identify and analyze sequences from Saccharomyces cerevisiae and related sequences from other organisms. Nucleic Acids Res., 32 (Database issue), D311-D314.
29. Birney,E., Andrews,D., Bevan,P., Caccamo,M., Cameron,G., Chen,Y., Clarke,L., Coates,G., Cox,T., Cuff,J. et al. (2004) Ensembl 2004. Nucleic Acids Res., 32 (Database issue), D468-D470.
30. Twigger,S., Lu,J., Shimoyama,M., Chen,D., Pasko,D., Long,H., Ginster,J., Chen,C.F., Nigam,R., Kwitek,A. et al. (2002) Rat Genome Database (RGD): mapping disease onto the genome. Nucleic Acids Res. 30, 125-128.
31. Bult,C.J., Blake,J.A., Richardson,J.E., Kadin,J.A., Eppig,J.T., Baldarelli,R.M., Barsanti,K., Baya,M., Beal,J.S., Boddy,W.J. et al. (2004) The Mouse Genome Database (MGD): integrating biology with the genome. Nucleic Acids Res., 32 (Database issue), D476-D481.
32. Kasprzyk,A., Keefe,D., Smedley,D., London,D., Spooner,W., Melsopp,C., Hammond,M., Rocca-Serra,P., Cox,T. and Birney,E. (2004) EnsMart: a generic system for fast and flexible access to biological data. Genome Res., 14, 160-169.
33. Krieger,C.J., Zhang,P., Mueller,L.A., Wang,A., Paley,S., Arnaud,M., Pick,J., Rhee,S.Y. and Karp,P.D. (2004) MetaCyc: a multiorganism database of metabolic pathways and enzymes. Nucleic Acids Res., 32 (Database issue), D438-D442.