Bi-CoPaM ensemble clustering application to five Escherichia coli bacterial datasets

European Signal Processing Conference

Volumn , Issue , 2014, Pages 2485-2489

  Abu Jamous, Basel ^a   Fa, Rui ^a   Roberts, David J ^b   Nandi, Asoke K ^a,c  

^a BRUNEL UNIVERSITY   (United Kingdom)

^b UNIVERSITY OF OXFORD   (United Kingdom)

^c UNIVERSITY OF JYVÄSKYLÄ   (Finland)

Author keywords

Bi CoPaM; Escherichia coli bacteria; gene clustering; microarray data analysis

Indexed keywords

ESCHERICHIA COLI; GENES; MACHINERY;

AVERAGE PROFILES; BIOLOGICAL PROCESS; ENSEMBLE CLUSTERING; ESCHERICHIA COLI BACTERIA; GENE CLUSTERING; MICROARRAY DATA ANALYSIS; MICROARRAY DATA SETS; PRE-FILTERING;

SIGNAL PROCESSING;

EID: 84911881839     PISSN: 22195491     EISSN: None     Source Type: Conference Proceeding    
DOI: None     Document Type: Conference Paper

References (19)

1. B. Palsson and K. Zengler, "The challenges of integrating multi-omic data sets," Nature Chemical Biology, vol. 6, pp. 787-789, 2010.
2. P. Cahan, F. Rovegno, D. Mooney, J. C. Newman, G. S. Laurent and T. A. McCaffrey, "Meta-analysis of microarray results: challenges, opportunities, and recommendations for standardization," Gene, vol. 401, no. 1-2, p. 12-18, 2007.
3. R. Nilsson, I. J. Schultz, E. L. Pierce, K. A. Soltis, A. Naranuntarat, D. M. Ward, J. M. Baughman, P. N. Paradkar, P. D. Kingsley, V. C. Culotta, J. Kaplan, J. Palis, B. H. Paw and V. K. Mootha, "Discovery of Genes Essential for Heme Biosynthesis through Large-Scale Gene Expression Analysis," Cell Metabolism, vol. 10, pp. 119-130, 2009.
4. S. Monti, P. Tamayo, J. Mesirov and T. Golub, "Consensus clustering - A resampling-based method for class discovery and visualization of gene expression microarray data," Machine Learning, vol. 52, p. 91-118, 2003.
5. B. Abu-Jamous, R. Fa, D. J. Roberts and A. K. Nandi, "Paradigm of Tunable Clustering using Binarization of Consensus Partition Matrices (Bi-CoPaM) for Gene Discovery," PLOS ONE, vol. 8, no. 2, 2013.
6. B. Abu-Jamous, R. Fa, D. J. Roberts and A. K. Nandi, "Identification of genes consistently co-expressed in multiple microarrays by a genome-wide approach," in The Proceedings of the 38th International Conference on Acoustics, Speech, and Signal Processing (ICASSP), Vancouver, Canada, 2013.
7. B. Abu-Jamous, R. Fa, D. J. Roberts and A. K. Nandi, "Yeast gene CMR1/YDL156W is consistently co-expressed with genes participating in DNA-metabolic processes in a variety of stringent clustering experiments," Journal of the Royal Society Interface, vol. 10, no. 81, 2013.
8. J. M. Pena, J. A. Lozano and P. Larranaga, "An empirical comparison of four initialization methods for the K-Means algorithm," Pattern Recognition Letters, vol. 20, no. 10, pp. 1027-1040, 1999.
9. M. B. Eisen, P. T. Spellman, P. O. Brown and D. Botstein, "Cluster analysis and display of genome-wide expression patterns," in Proc Natl Acad Sci (PNAS), 1998.
10. B. Abu-Jamous, R. Fa, D. J. Roberts and A. K. Nandi, "Hybrid binarisation technique for the Bi-CoPaM method," in Proceedings of the 2013 Constantinides International Workshop on Signal Processing (CIWSP-2013), London, UK, 2013.
11. J. Lee, X.-S. Zhang, M. Hegde, W. E. Bentley, A. Jayaraman and T. K. Wood, "Indole cell signaling occurs primarily at low temperatures in Escherichia coli," The ISME Journal, vol. 2, p. 1007-1023, 2008.
12. M. E. Laubacher and S. E. Ades, "The Rcs phosphorelay is a cell envelope stress response activated by peptidoglycan stress and contributes to intrinsic antibiotic resistance," Journal of Bacteriology, vol. 190, no. 6, p. 2065-2074, 2008.
13. A. K. Holm, L. M. Blank, M. Oldiges, A. Schmid, C. Solem, P. R. Jensen and G. N. Vemuri, "Metabolic and transcriptional response to cofactor perturbations in Escherichia coli," The Journal of Biological Chemistry, vol. 285, no. 23, p. 17498-17506, 2010.
14. K. Arunasri, M. Adil, K. V. Charan, C. Suvro, S. H. Reddy and S. Shivaji, "Effect of simulated microgravity on E. coli K12 MG1655 growth and gene expression," PLOS ONE, vol. 8, no. 3, 2013.
15. S. Kamen͈ek and D. Z;gur-Bertok, "Global transcriptional responses to the bacteriocin colicin M in Escherichia coli," BMC Microbiology, vol. 13, 2013.
16. L. Kaufman and P. J. Rousseeuw, Finding groups in data: an introduction to cluster analysis, John Wiley &Sons, Inc., 2005.
17. J. H. Ward, "Hierarchical grouping to optimize an objective function," Journal of the American statistical association, vol. 58, no. 301, pp. 236-244, 1963.
18. X. Xiao, E. R. Dow, R. Eberhart, Z. B. Miled and R. J. Oppelt, "Gene clustering using self-organizing maps and particle swarm optimization," in IEEE-IPDPS, Indianapolis, 2003.
19. C. H. Wade, M. A. Umbarger and M. A. McAlear, "The budding yeast rRNA and ribosome biosynthesis (RRB) regulon contains over 200 genes," Yeast, vol. 23, p. 293-306, 2006.