GenePublisher: Automated analysis of DNA microarray data

Nucleic Acids Research

Volumn 31, Issue 13, 2003, Pages 3471-3476

  Knudsen, Steen ^a   Workman, Christopher ^a   Sicheritz Ponten, Thomas ^a,b   Friis, Carsten ^a  

^a TECHNICAL UNIVERSITY OF DENMARK   (Denmark)

^b UPPSALA UNIVERSITY   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

DNA;

ACCESS TO INFORMATION; ARTICLE; AUTOMATION; CONTROLLED STUDY; DATA ANALYSIS; DNA MICROARRAY; GENE SEQUENCE; INTERNET; NUCLEIC ACID DATABASE; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROMOTER REGION; SIGNAL TRANSDUCTION; STATISTICAL ANALYSIS; CLUSTER ANALYSIS; COMPUTER PROGRAM; GENE EXPRESSION PROFILING; GENETIC DATABASE; METABOLISM; METHODOLOGY; REGULATORY SEQUENCE;

AUTOMATION; CLUSTER ANALYSIS; DATABASES, GENETIC; GENE EXPRESSION PROFILING; INTERNET; METABOLISM; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PROMOTER REGIONS (GENETICS); REGULATORY SEQUENCES, NUCLEIC ACID; SIGNAL TRANSDUCTION; SOFTWARE;

EID: 0042121251     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkg629     Document Type: Article

References (18)

1. The Chipping Forecast II (2002) Nature Genet., 32.
2. Liu,G., Loraine,A.E., Shigeta,R., Cline,M., Cheng,J., Valmeekam,V., Sun,S., Kulp,D. and Siani-Rose,M.A. (2003) NetAffx: Affymetrix probesets and annotations. Nucleic Acids Res., 31, 82-86.
3. 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.
4. 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.
5. Workman,C., Jensen,L.J., Jarmer,H., Berka,R., Saxild,H.H., Gautier,L., Nielsen,C., Nielsen,H.B., Brunak,S. and Knudsen,S. (2002) A new non-linear method for reducing variance between DNA microarray experiments. Genome Biol., 3, research0048.1-0048.16.
6. Li,C. and Wong,W.H. (2001) Model-based analysis of oligonucleotide arrays: Expression index computation and outlier detection. Proc. Natl Acad. Sci. USA, 98, 31-36.
7. Fellenberg,K., Hauser,N.C., Brors,B., Neutzner,A., Hoheisel,J.D. and Vingron,M. (2001) Correspondence analysis applied to microarray data. Proc. Natl Acad. Sci. USA, 98, 10781-10786.
8. The Gene Ontology Consortium (2000) Gene Ontology: tool for the unification of biology. Nature Genet., 25, 25-29.
9. Kanehisa,M., Goto,S., Kawashima,S. and Nakaya,A. (2002) The KEGG databases at GenomeNet. Nucleic Acids Res., 30, 42-46.
10. Krull,M., Voss,N., Choi,C., Pistor,S., Potapov,A. and Wingender,E. (2003) TRANSPATH: an integrated database on signal transduction and a tool for array analysis. Nucleic Acids Res., 31, 97-100.
11. Jensen,L.J., Gupta,R., Blom,N., Devos,D., Tamames,J., Kesmir,C., Nielsen,H., Staerfeldt,H.H., Rapacki,K., Workman,C. et al. (2002) Ab initio rediction of human orphan protein function from post-translational modifications and localization features. J. Mol. Biol., 319, 1257-1265.
12. Sokal,R.R. and Sneath,P.H.A. (1963) Principles of Numerical Taxonomy, Freeman, San Francisco.
13. Yeung,K.Y., Haynor,D.R. and Ruzzo,W.L.(2001) Validating clustering for gene expression data. Bioinformatics, 17, 309-318.
14. Eisen,M.B., Spellman,P.T., Brown,P.O. and Botstein,D. (1998) Cluster analysis and display of genome-wide expression patterns. Proc. Natl Acad. Sci. USA, 95, 14863-14868.
15. Hubbard,T., Barker,D., Birney,E., Cameron,G., Chen,Y., Clark,L., Cox,T., Cuff,J., Curwen,V, Down,T. et al. (2002) The Ensembl genome database project. Nucleic Acids Res., 30, 38-41.
16. Jensen,L.J. and Knudsen,S. (2000) Automatic discovery of regulatory patterns in promoter regions based on whole cell expression data and functional annotation. Bioinformatics, 16, 326-333.
17. Lawrence,C.E., Altschul,S.F., Boguski,M.S., Liu,J.S., Neuwald,A.F., and Wootton,J.C. (1993) Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment. Science, 262, 208-214.
18. Matys,V., Fricke,E., Geffers,R., Gossling,E., Haubrock,M., Hehl,R., Hornischer,K., Karas,D., Kel,A.E., Kel-Margoulis,O.V et al. (2003) TRANSFAC: transcriptional regulation, from patterns to profiles. Nucleic Acids Res., 31, 374-378.