GARBAN: Genomic analysis and rapid biological annotation of cDNA microarray and proteomic data

Bioinformatics

Volumn 19, Issue 16, 2003, Pages 2158-2160

  Martínez Cruz, Luiz A ^a   Rubio, Angel ^b   Martínez Chantar, María L ^a   Labarga, Alberto ^b   Barrio, Isabel ^b   Podhorski, Adam ^b   Segura, Victor ^b   Sevilla Campo, José L ^b   Avila, Matías A ^a   Mato, Jose M ^a  

^a UNIVERSITY OF NAVARRA   (Spain)

^b CEIT   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA;

ANALYTIC METHOD; ARTICLE; AUTOMATION; CLASSIFICATION; CLUSTER ANALYSIS; COMPARATIVE STUDY; COMPUTER ANALYSIS; COMPUTER GRAPHICS; COMPUTER INTERFACE; COMPUTER PROGRAM; DATA ANALYSIS; DNA MICROARRAY; GENE EXPRESSION; GENE FUNCTION; GENETIC ANALYSIS; GENOME ANALYSIS; MOLECULAR BIOLOGY; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEOMICS; STANDARD;

EID: 10744223802     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/btg291     Document Type: Article

References (17)

1. Apweiler,R., Attwood,T.K., Bairoch,A., Bateman,A., Birney,E., Biswas,M., Bucher,P., Cerutti,L., Corpet,F., Croning,M.D. et al. (2001) The InterPro database, an integrated documentation resource for protein families, domains and functional sites. Nucleic Acids Res., 29, 37-40.
2. Debouck,C. and Goodfellow,P.N. (1999) DNA microarrays in drug discovery and development. Nat. Genet., 21(Suppl. 1), 48-50.
3. Diehn,M., Sherlock,G., Binkley,G., Jin,H., Matese,J.C., Hernandez-Boussard,T., Rees,C.A., Cherry,J.M., Botstein,D., Brown,P.O. and Alizadeh,A.A. (2003) SOURCE: a unified genomic resource of functional annotations, ontologies, and gene expression data. Nucleic Acids Res., 31, 219-223
4. Dougherty,E.R., Barrera,J., Brun,M., Kim,S., Cesar,R.M., Chen,Y., Bittner,M. and Trent,J.M. (2002) Inference from clustering with application to gene-expression microarrays. J. Comput. Biol., 9, 105-126.
5. Doniger,S.W., Salomonis,N., Dahlquist,K.D, Vranizan,K., Lawlor,S.C. and Conklin,B.R. (2003) MAPPFinder: using Gene Ontology and GenMAPP to create a global gene-expression profile from microarray data. Genome Biol., 4, R7.
6. DeRisi,J.L., Iyer,V. and Brown,P. (1997) Exploring the metabolic and genetic control of gene expression on a genomic scale. Science, 278, 680-686.
7. 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.
8. Khan,J., Saal,L.H., Bittner,M.L., Chen,Y., Trent,J.M. and Meltzer,P.S. (1999) Expression profiling in cancer using cDNA microarrays. Electrophoresis, 20, 223-229.
9. Kohonen,T. (2001) Self-Organizing Maps. Springer Series in Information Sciences, Vol. 30, Springer-Verlag, Berlin-Heidelberg.
10. Lemkin,P.F., Thornwall,G.C., Walton,K.D. and Hennighausen,L. (2000) The microarray explorer tool for data mining of cDNA microarrays: application for the mammary gland. Nucleic Acids Res., 28, 4452-4459.
11. Lukashin,A.V. and Fuchs,R. (2001) Analysis of temporal gene expression profiles: clustering by simulated annealing and determining the optimal number of clusters. Bioinformatics, 17, 405-414.
12. Marton,M.J., DeRisi,J.L., Bennett,H.A., Iyer,V.R., Meyer,M.R., Roberts,C.J., Stoughton,R., Burchard,J., Slade,D., Dai,H. et al. (1998) Drug target validation and identification of secondary drug target effects using DNA microarrays. Nat. Med., 4, 1293-1301.
13. Pruitt,K.D. and Maglott,D.R. (2001) RefSeq and LocusLink: NCBI gene-centered resources. Nucleic Acids Res., 29, 137-140.
14. Sherlock,G. (2000) Analysis of large-scale gene expression data. Curr. Opin. Immunol., 12, 201-205.
15. Spellman,P.T., Sherlock,G., Zhang,M.Q., Iyer,V.R., Anders,K., Eisen,M.B., Brown,P.O., Botstein,D. and Futcher,B. (1998) Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol. Biol. Cell., 9, 3273-3297.
16. Tamames,J., Clark,D., Herrero,J., Dopazo,J., Blaschke,C., Fernandez,J.M., Oliveros,J.C. and Valencia,A. (2002) Bioinformatics methods for the analysis of expression arrays: data clustering and information extraction. J. Biotechnol., 98, 269-283.
17. Tamayo,P., Slonim,D., Mesirov,J., Zhu,Q., Kitareewan,S., Dmitrovsky,E., Lander,E.S. and Golub,T.R. (1999) Interpreting patterns of gene expression with self-organizing maps: methods and application to hematopoietic differentiation. Proc. Natl Acad. Sci. USA, 96, 2907-2912.