Co-expressed gene assessment based on the path consistency algorithm: Operon detention in Escherichia coli

Conference Proceedings - IEEE International Conference on Systems, Man and Cybernetics

Volumn , Issue , 2009, Pages 4280-4286

  Saito, Shigeru ^a   Horimoto, Katsuhisa ^b  

^a INFOCOM Corporation   (Japan)

^b NATIONAL INSTITUTE OF ADVANCED INDUSTRIAL SCIENCE AND TECHNOLOGY AIST   (Japan)

Author keywords

Co expression; Gene expression profile; Gene regulation; Graphical model; Network inference

Indexed keywords

BIOLOGICAL INFORMATION; CAUSAL GRAPH; CO-EXPRESSION; EXPRESSED GENES; EXPRESSION PROFILE; GENE EXPRESSION PROFILES; GENE REGULATIONS; GRAPHICAL MODEL; IMPROVED ALGORITHM; MICROARRAY ANALYSIS; MICROARRAY DATA; NUMERICAL CALCULATION; PATH CONSISTENCY; REGULATORY SYSTEMS; SIMPLE METHOD;

ALGORITHMS; BIOACTIVITY; CYBERNETICS; ESCHERICHIA COLI; GENE EXPRESSION; GRAPHIC METHODS; LAWS AND LEGISLATION;

GENE EXPRESSION REGULATION;

EID: 74849126876     PISSN: 1062922X     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/ICSMC.2009.5346809     Document Type: Conference Paper

References (33)

1. D. K. Slonim, "From patterns to pathways: gene expression data analysis comes of age," Nat. Genet. 32, 502-508 (2002).
2. T. R. Hughes, M. J. Marton, A. R. Jones, C. J. Roberts, R. Stoughton, et al., "Functional discovery via a compendium of expression profiles," Cell 102, 109-126 (2000).
3. S. A. McCarroll, C. T. Murphy, S. Zou, S. D. Pletcher, C. S. Chin, et al., "Comparing genomic expression patterns across species identifies shared transcriptional profile in aging," Nat. Genet. 36, 197-204 (2004).
4. C. J. Wolfe, I. S. Kohane and A. J. Butte, "Systematic survey reveals general applicability of "guilt-by-association" within gene coexpression networks," BMC Bioinformatics 6, 227 (2005).
5. M. B. Eisen, P. T. Spellman, P. O. Brown and D. Botstein, "Cluster analysis and display of genome-wide expression patterns," Proc. Natl. Acad. Sci. USA 95, 14863-14868 (1998).
6. L. F. Wu, T. R. Hughes, A. P. Davierwala, M. D. Robinson, R. Stoughton, et al., "Large-scale prediction of Saccharomyces cerevisiae gene function using overlapping transcriptional clusters," Nat. Genet. 31, 255-265 (2002).
7. J. M. Stuart, E. Segal, D. Koller and S. K. Kim, "A gene-coexpression network for global discovery of conserved genetic modules," Science 302, 249-255 (2003).
8. A. Jain, Algorithms for clustering data. Prentice-Hall, Englewood Cliffs, 1988.
9. D. J. Allocco, I. S. Kohane and A. J. Butte, "Quantifying the relationship between co-expression, co-regulation, and gene function," BMC Bioinformatics 5, 18 (2004).
10. M. Moriyama, Y. Hoshida, M. Otsuka, S. Nishimura, N. Kato, et al., "Relevance network between chemosensitivity and transcriptome in human hepatoma cells," Mol. Cancer. Ther. 2, 199-205 (2003).
11. M. Bredel, C. Bredel, D. Juric, G. R. Harsh, H. Vogel, et al., "Functional network analysis reveals extended gliomagenesis pathway maps and three novel MYC-interacting genes in human gliomas," Cancer Res. 65, 8679-8689 (2005).
12. D. Sanoudou, J. N. Haslett, A. T. Kho, S. Guo, H. T. Gazda, et al., "Expression profiling reveals altered satellite cell numbers and glycolytic enzyme transcription in nemaline myopathy muscle," Proc. Natl. Acad. Sci. USA 100, 4666-4671 (2003).
13. B. H. Voy, J. A. Scharff, A. D. Perkins, A. M. Saxton, B. Borate, E. J. Chesler, L. K. Branstetter and M. A. Langston, "Extracting Gene Networks for Low-Dose Radiation Using Graph Theoretical Algorithms," PLoS Comput. Biol. 2, e89 (2006).
14. E. H. Simpson, "The interpretation of interaction in contingency tables," J. Roy. Statist. Soc. B, 13, 238-241 (1951).
15. H. Toh and K. Horimoto, "Inference of a genetic network by a combined approach of cluster analysis and graphical Gaussian modeling," Bioinformatics 18, 287- 297 (2002).
16. S. Aburatani, K. Goto, S. Saito, H. Toh and K. Horimoto, "ASIAN: a web server for inferring a regulatory network framework from gene expression profiles," Nucleic Acids Res. 33, W659-W664 (2005).
17. J. Whittaker, Graphical Models in Applied Multivariate Statistics. Wiley, New York, 1990.
18. A. de la Fuente, N. Bing, I. Hoeschele and P. Mendes, "Discovery of meaningful associations in genomic data using partial correlation coefficients," Bioinformatics 20, 3565-3574 (2004).
19. J. Schafer and K. Strimmer, "An empirical Bayes approach to inferring large-scale gene association networks," Bioinformatics 21, 754-764 (2005).
20. P. Spirtes, C. Glymour and R. Scheines Causation, Prediction, and Search (Springer Lecture Notes in Statistics, 2nd edition, revised). MIT Press, Cambridge, 2001.
21. J. Pearl, Probabilistic reasoning in intelligent systems: Networks of plausible inference. Morgan Kaufmann Publishers, Palo Alto, 1988.
22. H. Salgado, G. Moreno-Hagelsieb, T. F. Smith and J. Collado-Vides, "Operons in Escherichia coli: genome analyses and predictions," Proc. Natl. Acad. Sci. USA 97, 6652-6657 (2000).
23. C. Sabatti, L. Rohlin, M. K. Oh and J. C. Liao, "Co-expression patterm from DNA microarray experiments as a tool for operon prediction," Nucleic Acids Res. 30, 2886-2893 (2002).
24. T. W. Anderson, An Introduction to Multivariate Statistical Analysis. 2nd Edition, John Wiley & Sons, New York, 1984.
25. I. M. Keseler, J. Collado-Vides, S. Gama-Castro, J. Ingraham, S. Paley, I. T. Paulsen, M. Peralta-Gil and P. D. Karp, "EcoCyc: a comprehensive database resource for Escherichia coli," Nucleic Acids Res. 33, D334-D337 (2005).
26. J. A. Bernstein, A. B. Khodursky, P. H. Lin, S. Lin-Chao and S. N. Cohen, "Global analysis of mRNA decay and abundance in Escherichia coli at single-gene resolution using two-color fluorescent DNA microarrays," Proc. Natl. Acad. Sci. USA 99, 9697-9702 (2002).
27. J. A. Bernstein, P. H. Lin, S. N. Cohen and S. Lin-Chao, "Global analysis of Escherichia coli RNA degradosome function using DNA microarrays," Proc. Natl. Acad. Sci. USA 101, 2758-2763 (2004).
28. J. Courcelle, A. Khodursky, B. Peter, P. O. Brown and P. C. Hanawalt, "Comparative gene expression profiles following UV exposure in wildtype and SOS-deficient Escherichia coli," Genetics 158, 41-64 (2001).
29. A. B. Khodursky, B. J. Peter, N. R. Cozzarelli, D. Botstein, P. O. Brown and C. Yanofsky, "DNA microarray analysis of gene expression in response to physiological and genetic changes that affect tryptophan metabolism in Escherichia coli," Proc. Natl. Acad. Sci. USA 97, 12170-12175 (2000).
30. A. B. Khodursky, B. J. Peter, M. B. Schmid, J. DeRisi, D. Botstein, P. O. Brown and N. R. Cozzarelli, "Analysis of topoisomerase function in bacterial replication fork movement: use of DNA microarrays," Proc. Natl. Acad. Sci. USA 97, 9419-9424 (2000).
31. K. Lee, J. A. Bernstein and S. N. Cohen, "RNase G complementation of rne null mutation identifies functional interrelationships with RNase E in Escherichia coli," Mol. Microbiol. 43, 1445-1456 (2002).
32. K. Lee, X. Zhan, J. Gao, J. Qiu, Y. Feng, R. Meganathan, S. N. Cohen and G. Georgiou, "RraA. a protein inhibitor of RNase E activity that globally modulates RNA abundance in E. coli," Cell 114, 623-634 (2003).
33. T. H. Tani, A. Khodursky, R. M. Blumenthal, P. O. Brown and R. G. Matthews, "Adaptation to famine: a family of stationary-phase genes revealed by microarray analysis," Proc. Natl. Acad. Sci. USA 99, 13471-13476 (2002).