title: Investigation of self-organizing oscillator networks for use in clustering microarray data.
abstract: The self-organizing oscillator network (SOON) is a comparatively new clustering algorithm that does not require the knowledge of the number of clusters. The SOON is distance based, and its clustering behavior is different to density-based algorithms in a number of ways. This paper examines the effect of adjusting the control parameters of the SOON with four different datasets; the first is a (communications) modulation dataset representing one modulation scheme under a variety of noise conditions. This allows the assessment of the behavior of the algorithm with data varying between highly separable and nonseparable cases. The main thrust of this paper is to evaluate its efficacy in biological datasets. The second is taken from microarray experiments on the cell cycle of yeast, while the third and the fourth represent two microarray cancer datasets, i.e., the lymphoma and the liver cancer datasets. The paper demonstrates that the SOON is a viable tool to analyze these problems, and can add many useful insights to the biological data that may not always be available using other clustering methods.
authors.affiliation: Department of Electrical Engineering and Electronics, University of Liverpool, Liverpool, UK. sameh.salem@liverpool.ac.uk
authors.forename: S A
authors.initials: SA
authors.lastname: Salem
authors.forename: L B
authors.initials: LB
authors.lastname: Jack
authors.forename: A K
authors.initials: AK
authors.lastname: Nandi
mesh_terms: D000465:Algorithms; D014408:Biomarkers, Tumor / Q000032:analysis*; D016000:Cluster Analysis; D020869:Gene Expression Profiling / Q000379:methods*; D006801:Humans; D009363:Neoplasm Proteins / Q000032:analysis*; D009369:Neoplasms / Q000175:diagnosis / Q000378:metabolism*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D009991:Oscillometry / Q000379:methods
chemical_list: D014408:Biomarkers, Tumor; D009363:Neoplasm Proteins