Abstract
DNA microarray is a powerful tool and is widely used in genetics to monitor expression levels of thousands of genes in parallel. The gene expression process consists of three stages: gridding, segmentation and quantification. Gridding deals with finding areas in the microarray image which contain one spot using grid lines. This step can be done manually or automatically. In this paper, we propose an efficient and simple automatic gridding method for microarray image analysis. This method was implemented using MATLAB software and found very effective for gridding arrays with low intensity, poor quality spotsand tested by a number of microarray images. Results show that this method gives high accuracy of 76.9% improved to 98.6% when a preprocessing step is considered, rendering the method a promising technique for an efficient and automatic gridding the noisy microarray images.
Highlights
A DNA microarray is a powerful tool and is widely used in many research areas
This paper presents a fully automatic gridding method preceded by performing a noise removal step to overcome the effect of noise on the microarray image before starting the gridding process
We suggested a pre-processing step to the microarray image to overcome those problems.we presented the effect of the proposed gridding method before and after pre-processingon the results
Summary
A DNA microarray is a powerful tool and is widely used in many research areas. For biologists, genetic research, understanding and diagnosis of cancer and many other dangerous diseases, as well as discovering treatments of diseases, are among the most interesting areas where DNA microarray analysis may be extremely helpful[1]. Traditional methods in molecular biology generally work on one gene on a one-experiment basis, which means that the throughput is very limited and biologists can only be able to do such genetic analysis on a few genes at a time. Microarray technology makes it possible to measure the expression level of thousands of genes in a biological sample rapidly and efficiently on the slides[2]. The purpose of a microarray is to detect the presence and abundance of labelled nucleic acids in a biological sample, which will hybridize to the DNA on the array, and which can be detected via the label. Control and test RNA samples are processed on the same array using two different dye tagged probes
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