BarleyBase - An expression profiling database for plant genomics

Nucleic Acids Research

Volumn 33, Issue DATABASE ISS., 2005, Pages

  Shen, Lishuang ^a   Gong, Jian ^a   Caldo, Rico A ^b   Nettleton, Dan ^c   Cook, Dianne ^a,c   Wise, Roger P ^b   Dickerson, Julie A ^a  

^a Iowa State University   (United States)

^b IOWA STATE UNIVERSITY   (United States)

^c Iowa State University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARABIDOPSIS; ARTICLE; BARLEY; BARLEYBASE; DNA MICROARRAY; GENE EXPRESSION; GENE FUNCTION; GENE MAPPING; GENETIC DATABASE; GENOMICS; HYBRIDIZATION; INTERNET; MAIZE; NONHUMAN; PRIORITY JOURNAL; RICE; SEQUENCE ALIGNMENT; SOYBEAN; SPECIES COMPARISON; STATISTICAL ANALYSIS; WHEAT; ACCESS TO INFORMATION; BIOINFORMATICS; COMPUTER PREDICTION; DNA HYBRIDIZATION; EXPRESSED SEQUENCE TAG; GENE EXPRESSION PROFILING; INFORMATION PROCESSING; ONLINE SYSTEM; PLANT GENETICS;

ARABIDOPSIS; CEREALS; COMPUTER GRAPHICS; DATABASES, GENETIC; GENE EXPRESSION PROFILING; GENES, PLANT; GENOME, PLANT; GENOMICS; HORDEUM; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; SOFTWARE;

ARABIDOPSIS; GLYCINE MAX; HORDEUM VULGARE SUBSP. VULGARE; TRITICUM AESTIVUM; ZEA MAYS;

EID: 13444312020     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gki123     Document Type: Article

References (18)

1. Close,T., Wanamaker,S., Caldo,R., Turner,S., Ashlock,D., Dickerson,J., Wing,R., Muehlbauer,G., Kleinhofs,A. and Wise,R. (2004) A new resource for cereal genomics: 22K barley GeneChip comes of age. Plant Physiol., 134, 960-968.
2. Tang,X.Y., Gong,J., Xin,J.Q., Shen,L., Turner,S.M., Caldo,R.A., Nettleton,D., Wise,R.P. and Dickerson,J.A. (2004) Barleybase - an expression profiling database for cereal genomics. In Proceedings of the Plant and Animal Genome XII Conference, Jan 10-14 2004, San Diego, CA, p. 307.
3. Edgar,R., Domrachev,M. and Lash,A.E. (2002) Gene Expression Omnibus: NCBI gene expression and hybridization array data repository, Nucleic Acids Res., 30, 207-210.
4. Gollub,J., Ball,C.A., Binkley,G., Demeter,J., Finkelstein,D.B., Hebert,J.M., Hernandez-Boussard,T., Jin,H., Kaloper,M., Matese,J.C. et al. (2003) The Stanford Microarray Database: data access and quality assessment tools. Nucleic Acids Res., 31, 94-96.
5. Brazma,A., Parkinson,H., Sarkans,U., Shojatalab,M., Vilo,J., Abeygunawardena,N., Holloway,E., Kapushesky,M., Kemmeren,P., Lara,G.G. et al. (2003) ArrayExpress - a public repository for microarray gene expression data at the EBI. Nucleic Acids Res., 31, 68-71.
6. Rhee,S.Y., Beavis,W., Berardini,T.Z., Chen,G., Dixon,D., Doyle,A., Garcia-Hernandez,M., Huala,E., Lander,G., Montoya,M. et al. (2003) The Arabidopsis Information Resource (TAIR): a model organism database providing a centralized, curated gateway to Arabidopsis biology, research materials and community. Nucleic Acids Res., 31, 224-228.
7. Craigon,D.J., James,N., Okyere,J., Higgins,J., Jotham,J. and May,S. (2004) NASCArrays: a repository for microarray data generated by NASC's transcriptomics service. Nucleic Acids Res., 32, D575-D577.
8. Dong,Q., Schlueter,S.D. and Brendel,V. (2004) PlantGDB, plantgenome database and analysis tools. Nucleic Acids Res., 32 D354-D359.
9. Ware,D., Jaiswal,P., Ni,J., Pan,X., Chang,K., Clark,K., Teytelman,L., Schmidt,S., Zhao,W., Cartinhour,S.et al. (2002) Gramene: a resource for comparative grass genomics. Nucleic Acids Res. 30, 103-105.
10. Matthews,D.E., Carollo,V.L., Lazo,G.R. and Anderson,O.D. (2003) GrainGenes, the genome database for small-grain crops. Nucleic Acids Res., 31, 183-186.
11. The Plant OntologyP™ Consortium (2002) The Plant Ontology™ Consortium and Plant Ontologies. Comp. Funct. Genomics, 3, 137-142.
12. Brazma,A., Hingamp,P., Quackenbush,J., Sherlock,G., Spellman,P., Stoeckert,C., Aach,J., Ansorge,W., Ball,C.A., Causton,H.C. et al. (2001) Minimum information about a microarray experiment (MIAME) - toward standards for microarray data. Nature Genet., 29, 365-371.
13. Ihaka,R. and Gentleman,R. (1996) R: a language for data analysis and graphics, J. Comput. Graphical Stat., 5, 299-314.
14. Gautier,L., Cope,L., Bolstad,B. and Irizarry,R. (2004) Affy - analysis of Affymetrix GeneChip data at the probe level. Bioinformatics, 20, 307-315.
15. Affymetrix (2001) Statistical Algorithms Reference Guide Affymetrix Inc., Santa Clara, CA.
16. Altschul,S., Gish,W., Miller,W., Myers,E. and Lipman,D. (1990) Basic local alignment search tool. J. Mol. Biol., 215, 403-410.
17. Saeed,A., Sharov,V., White,J., Li,J., Liang,W., Bhagabati,N., Braisted,J., Klapa,M., Currier,T., Thiagarajan,M. et al. (2003) TM4: a free, open-source system for microarray data management and analysis, Biotechniques, 34, 374-378.
18. Saal,L.H., Troein,C., Vallon-Christersson,J., Gruvberger,S., Borg,Å. and Peterson,C. (2002) BioArray software environment: a platform for comprehensive management and analysis of microarray data. Genome Biol., 3, software0003.0001-software0003.0006.