Abstract: Microarrays have become the effective, broadly used tools in biological and medical research to address a wide range of problems, including classification of disease subtypes and tumors. Many statistical methods are available for analyzing and systematizing these complex data into meaningful information, and one of the main goals in analyzing gene expression data is the detection of samples or genes with similar expression patterns. In this paper, we express and compare the performance of several clustering methods based on data preprocessing including strategies of normalization or noise clearness. We also evaluate each of these clustering methods with validation measures for both simulated data and real gene expression data. Consequently, clustering methods which are common used in microarray data analysis are affected by normalization and degree of noise and clearness for datasets.
Abstract: The goal of Gene Expression Analysis is to understand the processes that underlie the regulatory networks and pathways controlling inter-cellular and intra-cellular activities. In recent times microarray datasets are extensively used for this purpose. The scope of such analysis has broadened in recent times towards reconstruction of gene networks and other holistic approaches of Systems Biology. Evolutionary methods are proving to be successful in such problems and a number of such methods have been proposed. However all these methods are based on processing of genotypic information. Towards this end, there is a need to develop evolutionary methods that address phenotypic interactions together with genotypic interactions. We present a novel evolutionary approach, called Phenomic algorithm, wherein the focus is on phenotypic interaction. We use the expression profiles of genes to model the interactions between them at the phenotypic level. We apply this algorithm to the yeast sporulation dataset and show that the algorithm can identify gene networks with relative ease.
Abstract: Cancers could normally be marked by a number of
differentially expressed genes which show enormous potential as
biomarkers for a certain disease. Recent years, cancer classification
based on the investigation of gene expression profiles derived by
high-throughput microarrays has widely been used. The selection of
discriminative genes is, therefore, an essential preprocess step in
carcinogenesis studies. In this paper, we have proposed a novel gene
selector using information-theoretic measures for biological
discovery. This multivariate filter is a four-stage framework through
the analyses of feature relevance, feature interdependence, feature
redundancy-dependence and subset rankings, and having been
examined on the colon cancer data set. Our experimental result show
that the proposed method outperformed other information theorem
based filters in all aspect of classification errors and classification
performance.