Gene expression extraction in cervical cancer by segmentation of microarray images using a novel fuzzy method

Abstract

ABSTRACT It is necessary to obtain gene expression values to identify gene biomarkers involved in all types of cancers, and microarray data is one of the best data for this purpose. In order to extract gene expression values from microarray images that have different challenges. This article presents a completely automatic and comprehensive method that can deal with the various challenges in these images and obtain gene expression values with high accuracy. A pre-processing approach is proposed for contrast enhancement using a genetic algorithm and for removing noise and artefacts in microarray cells using wavelet transform based on a complex Gaussian scaling model. For each point, the coordinate centre is determined using Self Organising Maps. Then, using a new hybrid model based on the Fuzzy Local Information Gaussian Mixture Model (FLIGMM), the position of each spot is accurately determined. In this model, various features are obtained using local information about pixels, considering the pixel neighbourhood correlation coefficient. Finally, the gene expression values are obtained. The performance of the proposed algorithm was evaluated using real microarray images of cervical cancer from the GMRCL microarray dataset as well as simulated images. The results show that the proposed algorithm achieves 90.91% and 98% accuracy in segmenting microarray spots for noiseless and noisy spots, respectively.