Predicting gene ontology biological process from temporal gene expression patterns

Genome Research

Volumn 13, Issue 5, 2003, Pages 965-979

  Lægreid, Astrid ^a   Hvidsten, Torgeir R ^a   Midelfart, Herman ^a   Komorowski, Jan ^a,b   Sandvik, Arne K ^a  

^a NORWEGIAN UNIVERSITY OF SCIENCE AND TECHNOLOGY   (Norway)

^b UPPSALA UNIVERSITY   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CLASSIFICATION; CONTROLLED STUDY; DATA BASE; DNA MICROARRAY; GENE EXPRESSION PROFILING; GENE EXPRESSION SYSTEM; GENE FUNCTION; GENE IDENTIFICATION; HUMAN; HYPOTHESIS; LEARNING; NONHUMAN; NUCLEOTIDE SEQUENCE; PREDICTION; PRIORITY JOURNAL; SEQUENCE HOMOLOGY; UNINDEXED SEQUENCE; VALIDATION PROCESS;

ANIMALS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENES; GENES, BACTERIAL; GENES, INSECT; GENES, NEOPLASM; HUMANS; MICE; MODELS, GENETIC; PREDICTIVE VALUE OF TESTS; RATS; SENSITIVITY AND SPECIFICITY; SEQUENCE HOMOLOGY, NUCLEIC ACID; TERMINOLOGY; TIME;

EUKARYOTA;

EID: 0038781869     PISSN: 10889051     EISSN: None     Source Type: Journal    
DOI: 10.1101/gr.1144503     Document Type: Article

References (26)

1. Adachi, Y. and Yanagida, M. 1989. Higher order chromosome structure is affected by cold-sensitive mutations in a Schizosaccharomyces pombe gene crm1+ which encodes a 115-kD protein preferentially localized in the nucleus and its periphery. J. Cell Biol. 108: 1195-1207.
2. Brown, M.P., Grundy, W.N., Lin, D., Cristianini, N., Sugnet, C.W., Furey, T.S., Ares Jr., M., and Haussler, D. 2000. Knowledge-based analysis of microarray gene expression data by using support vector machines. Proc. Natl. Acad. Sci. 97: 262-267.
3. Cho, R.J., Huang, M., Campbell, M.J., Dong, H., Steinmetz, L., Sapinoso, L., Hampton, G., Elledge, S.J., Davis, R.W., and Lockhart, D.J. 2001. Transcriptional regulation and function during the human cell cycle. Nat. Genet. 27: 48-54.
4. Davis, S.R. and Cousins, R.J. 2000. Metallothionein expression in animals: A physiological perspective on function. J. Nutr. 130: 1085-1088.
5. 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. 95: 14863-14868.
6. Everitt, B.S. 1992. The analysis of contingency tables. In Monographs on statistics and applied probability, 2nd ed. vol. 45, pp. 1-164. Chapman & Hall, London, UK.
7. The Gene Ontology Consortium (Ashburner, M., Ball, C.A., Blake, J.A., Botstein, D., Butler, H., Cherry, J.M., Davis, A.P., Dolinski, K., Dwight, S.S., Eppig, J.T., et al.). 2000. Gene ontology: Tool for the unification of biology. Nat. Genet. 25: 25-29.
8. Halushka, P.V., Allan, C.J., and Davis-Bruno, K.L. 1995. Thromboxane A2 receptors. J. Lipid Mediat. Cell Signal. 12: 361-378.
9. Hardy, P., Dumont, I., Bhattacharya, M., Hou, X., Lachapelle, P., Varma, D.R., and Chemtob, S. 2000. Oxidants, nitric oxide and prostanoids in the developing ocular vasculature: A basis for ischemic retinopathy. Cardiovasc. Res. 47: 489-509.
10. Hvidsten, T.R., Komorowski, J., Sandvik, A.K., and Lægreid, A. 2001. Predicting gene function from gene expressions and ontologies. Pac. Symp. Biocomput. (eds. R.B. Altman et al.) pp. 299-310. World Scientific Publishing, Singapore.
11. Iyer, V.R., Eisen, M.B., Ross, D.T., Schuler, G., Moore, T., Lee, J.C., Trent, J.M., Staudt, L.M., Hudson Jr., J., Boguski, M.S., et al. 1999. The transcriptional program in the response of human fibroblasts to serum. Science 283: 83-87.
12. Koga, H., Matsui, S., Hirota, T., Takebayashi, S., Okumura, K., and Saya, H. 1999. A human homolog of Drosophila lethal(3)malignant brain tumor (1(3)mbt) protein associates with condensed mitotic chromosomes. Oncogene 18: 3799-3809.
13. Komorowski, J. 1999. Rough Sets - A tutorial. In Rough-fuzzy hybridization - A new trend in decision making (eds. S.K. Pal and A. Skowron), pp. 3-98. Singapore Pte Ltd., Springer Verlag, Singapore.
14. Komorowski, J., Skowron, A., and Øhrn, A. 2002. ROSETTA Rough Set software system. In Handbook of data mining and knowledge discovery (eds. W. Kløsgen and J. Zytkow), pp. 554-559. Oxford University Press, New York, NY.
15. Midelfart, H., Lægreid, A., and Komorowski, J. 2001. Classification of gene expression data in an ontology. In International Symposium on Medical Data Analysis (eds. J. Crespo et al.), pp. 186-194. Springer-Verlag, Vienna, Austria.
16. Pawlak, Z. 1991. Rough Sets. Theory Decision Lib. 9: 1-229.
17. Ravnik, S.E. and Wolgemuth, D.J. 1996. The developmentally restricted pattern of expression in the male germ line of a murine cyclin A, cyclin A2, suggests roles in both mitotic and meiotic cell cycles. Dev. Biol. 173: 69-78.
18. Schena, M., Shalon, D., Davis, R.W., and Brown, P.O. 1995. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270: 467-470.
19. Schroepfer Jr., G.J. 2000. Oxysterols: Modulators of cholesterol metabolism and other processes. Physiol. Rev. 80: 361-554.
20. Shatkay, H., Edwards, S., Wilbur, W.J., and Boguski, M. 2000. Genes, themes and microarrays: Using information retrieval for large-scale gene analysis. Proc. Int. Conf. Intell. Syst. Mol. Biol. 8: 317-328.
21. Skowron, A., Komorowski, J., Pawlak, Z., and Polkowski, L. 2002. A Rough Set perspective on data and knowledge. In Handbook of data mining and knowledge discovery (eds. W. Kløsgen and J. Zytkow), pp. 134-149. Oxford University Press, New York, NY.
22. Stanton, L.W., Garrard, L.J., Damm, D., Garrick, B.L., Lam, A., Kapoun, A.M., Zheng, Q., Protter, A.A., Schreiner, G.F., and White, R.T. 2000. Altered patterns of gene expression in response to myocardial infarction. Circ. Res. 86: 939-945.
23. Torgo, L. 1993. In Proceedings of the European Conference on Machine Learning (ed. P.B. Brazdil), pp. 185-196. Springer Verlag, Vienna, Austria.
24. Wu, L.F., Hughes, T.R., Davierwala, A.P., Robinson, M.D., Stoughton, R., and Altschuler, S.J. 2002. Large-scale prediction of Saccharomyces cerevisiae gene function using overlapping transcriptional clusters. Nat. Genet. 31: 255-265.
25. Zhang, H., Kobayashi, R., Galaktionov, K., and Beach, D. 1995. p19Skp1 and p45Skp2 are essential elements of the cyclin A-CDK2 S phase kinase. Cell 82: 915-925.
26. Zhu, X., Mancini, M.A., Chang, K.H., Liu, C.Y., Chen, C.F., Shan, B., Jones, D., Yang-Feng, T.L., and Lee, W.H. 1995. Characterization of a novel 350-kilodalton nuclear phosphoprotein that is specifically involved in mitotic-phase progression. Mol. Cell. Biol. 15: 5017-5029.