Interpreting microarray data to build models of microbial genetic regulation networks

Proceedings of SPIE - The International Society for Optical Engineering

Volumn 4623, Issue , 2002, Pages 27-37

  Sokhansanj, Bahrad A ^a   Garnham, Janine B ^a   Fitch, J Patrick ^a  

^a LAWRENCE LIVERMORE NATIONAL LABORATORY   (United States)

Author keywords

Bacteria; Fuzzy logic; Gene regulation; Microarrays; Modeling and simulation

Indexed keywords

BACTERIA; COMPUTER SIMULATION; DNA; FUZZY SETS; GENES; JAVA PROGRAMMING LANGUAGE; RNA;

GENE REGULATION; MICROARRAYS;

MICROBIOLOGY;

EID: 0036399968     PISSN: 0277786X     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1117/12.469450     Document Type: Conference Paper

References (20)

1. J.P. Fitch and B. Sokhansanj, Genomic engineering: moving beyond DNA sequence to function, Proc. IEEE, 88, pp. 1949-1971, 2000.
2. D.J. Lockhart, H. Dong, M.C. Byrne, M.T. Follettie, M.V. Gallo, M.S. Chee, M. Mittmann, C. Wang, M. Kobyashi, H. Horton, and E.L. Brown, Expression monitoring by hybridization to high-density oligonucleotide arrays, Nat. Biotechnol., 14, 1675-1680, 1996.
3. J.L. DeRisi, V.R. Iyer, and P.O. Brown, Exploring the metabolic and genetic control of gene expression on a genomic scale, Science, 278, pp. 680-686, 1997.
4. Y. Chen, E.R. Dougherty, and M.L. Bittner, Ratio-based decisions and the quantitative analysis of cDNA microarray images, J. Biomedical Optics, 2, pp. 364-374, 1997.
5. H. Hanspeter, D. Beule, S. Kielbasa, J. Korbel, C. Sers, A. Malik, H. Eickhoff, H. Lehrach, J. Schuchhardt, Extracting information from cDNA arrays, Chaos, 11, pp. 98-107, 2001.
6. G.C. Tseng, O. Min-Kyu, L. Rohlin, J.C. Liao, and W.H. Wong, Issues in cDNA microarray analysis: quality filtering, channel normalization, models of variations and assessment of gene effects, Nucleic Acids Res., 29, pp. 2549-2557, 2001.
7. M.B. Eisen, P.T. Spellman, P.O. Brown, and D. Botstein, Cluster analysis and display of genome-wide expresion patterns, Proc. Natl. Acad. Sci. USA, 95, pp. 14863-14868, 1998.
8. L.A. Zadeh, Outline of a new approach to the analysis of complex systems and decision processes, IEEE Trans. Syst. Man. Cybernet., 3, pp. 28-44, 1973.
9. J. DeRisi, L. Penland, P.O. Brown, M.L. Bittner, P.S. Meltzer, M. Ray, Y. Chen, Y.A. Su, and J.M. Trent, Use of a cDNA microarray to analyse gene expression patterns in human cancer, Nat. Genet., 14, pp. 457-460.
10. T. Ideker, V. Thorsson, A.F. Siegel, L.E. Hood, Testing for differentially-expressed genes by maximum-likelihood analysis of microarray data, J. Comp. Biol., 7, pp. 805-817, 2000.
11. Statistical analysis of gene expression from cDNA microarray experiments, http://www.statsci.org/micrarra/. Laboratory for the statistical analysis of microarrays, http://www-stat.stanford.edu/̃tibs/lab/index.html. Terry Speed s microarray data analysis group, http://www.stat.berkeley.edu/users/terry/zarray/Html/index.html.
12. T. Ideker, V. Thorsson, J.A. Ranish, R. Christmas, J. Buhler, J.K. Eng, R. Burngarner, D.R. Goodlett, R. Aebersold, and L. Hood, Integrated genomic and proteomic analyses of a systematically perturbed metabolic network, Science, 292, pp. 929-934, 2001.
13. M.D. Ermolaeva, O. White, and S.L. Salzberg, Prediction of operons in microbial genomes, Nucleic Acids Res., 29, pp. 1216-1221, 2001.
14. L.A. Zadeh, Fuzzy sets, Information and Control, 8, pp. 338-352, 1965.
15. J.M. Mendel, Fuzzy logic systems for engineering: a tutorial, Proc. IEEE, 83, 345-377, 1995.
16. H. Zimmerman, Fuzzy Set Theory and its Applications, Kluwer, Boston, Massuchessets, 1999.
17. W.E. Combs and J.E. Andrews, Combinatorial rule explosion eliminated by a fuzzy rule configuration, IEEE Trans. Fuzzy Syst., 6, pp. 1-11, 1998.
18. L.A. Zadeh, Fuzzy sets as a basis for a theory of possibility, Fuzzy Sets and Systems, 1, pp. 3-28, 1978.
19. P.J. Woolf and Y. Wang, A fuzzy logic approach to analyzing gene expression data, Physiol. Genomics, 3, pp. 9-15, 2000.
20. W.E. Combs, Comment on Combinatorial rule explosion eliminated by a fuzzy rule configuration, Authors reply, IEEE Trans. Fuzzy Syst., 7, pp. 417-418, 1999.