Spot Detection and Image Segmentation in DNA Microarray Data

Authors: Qin, Li¹; Rueda, Luis²; Ali, Adnan³; Ngom, Alioune²

Source: Applied Bioinformatics, Volume 4, Number 1, 2005 , pp. 1-11(11)

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Abstract:

Following the invention of microarrays in 1994, the development and applications of this technology have grown exponentially. The numerous applications of microarray technology include clinical diagnosis and treatment, drug design and discovery, tumour detection, and environmental health research. One of the key issues in the experimental approaches utilising microarrays is to extract quantitative information from the spots, which represent genes in a given experiment. For this process, the initial stages are important and they influence future steps in the analysis. Identifying the spots and separating the background from the foreground is a fundamental problem in DNA microarray data analysis. In this review, we present an overview of state-of-the-art methods for microarray image segmentation. We discuss the foundations of the circle-shaped approach, adaptive shape segmentation, histogram-based methods and the recently introduced clustering-based techniques. We analytically show that clustering-based techniques are equivalent to the one-dimensional, standard k-means clustering algorithm that utilises the Euclidean distance.

Keywords: Bioinformatics; Microarrays

Document Type: Research article

Affiliations: 1: 1 IBM Canada Ltd, Markham, Ontario, Canada 2: 2 School of Computer Science, University of Windsor, Windsor, Ontario, Canada 3: 3 Department of Biological Sciences, University of Windsor, Windsor, Ontario, Canada

Publication date: 2005-01-01