MDSM: microarray database schema matching using the Hungarian method

Current microarray databases use different terminologies and structures and thereby limit the sharing of data and collating of results between laboratories. Consequently, an effective integrated microarray data model is required. One important process to develop such an integrated database is schema matching. In this paper, we propose an effective schema matching approach called MDSM, to syntactically and semantically map attributes of different microarray schemas. The contribution from this work will be used later to create microarray global schemas. Since microarray data is complex, we use microarray ontology to improve the measuring accuracy of the similarity between attributes. The similarity relations can be represented as weighted bipartite graphs. We determine the best schema matching by computing the optimal matching in a bipartite graph using the Hungarian optimisation method. Experimental results show that our schema matching approach is effective and flexible to use in different kinds of database models such as; database schema, XML schema, and web site map. Finally, a case study on an existing public microarray schema is carried out using the proposed method.

Microarray analysis for gene expression that involves trace metals

Microarray plays a major role to identify the over- and under-expressed genes. It is a well-known fact that trace elements in our body play a major role in the metabolic processes of all living organisms. In this paper, the microarray studies related to major trace metals are reviewed. This review forms the basis for the converged effort to locate the genes that are either defective and destabilise the concentration of the trace metals or influenced by the changed concentration of the trace metals that are needed for proper functions of the human body, at different parts of the body.

Hybrid methods to select informative gene sets in microarray data classification

One of the key applications of microarray studies is to select and classify gene expression profiles of cancer and normal subjects. In this study, two hybrid approaches–genetic algorithm with decision tree (GADT) and genetic algorithm with neural network (GANN)–are utilized to select optimal gene sets which contribute to the highest classification accuracy. Two benchmark microarray datasets were tested, and the most significant disease related genes have been identified. Furthermore, the selected gene sets achieved comparably high sample classification accuracy (96.79% and 94.92% in colon cancer dataset, 98.67% and 98.05% in leukemia dataset) compared with those obtained by mRMR algorithm. The study results indicate that these two hybrid methods are able to select disease related genes and improve classification accuracy.

Heterologous microarray experiments used to identify the early gene response to heat stress in a coral reef fish

Coral reef fishes are expected to experience rising sea surface temperatures due to climate change. How well tropical reef fishes will respond to these increased temperatures and which genes are important in the response to elevated temperatures is not known. Microarray technology provides a powerful tool for gene discovery studies, but the development of microarrays for individual species can be expensive and time-consuming. In this study, we tested the suitability of a Danio rerio oligonucleotide microarray for application in a species with few genomic resources, the coral reef fish Pomacentrus moluccensis. Results from a comparative genomic hybridization experiment and direct sequence comparisons indicate that for most genes there is considerable sequence similarity between the two species, suggesting that the D. rerio array is useful for genomic studies of P. moluccensis. We employed this heterologous microarray approach to characterize the early transcriptional response to heat stress in P. moluccensis. A total of 111 gene loci, many of which are involved in protein processing, transcription, and cell growth, showed significant changes in transcript abundance following exposure to elevated temperatures. Changes in transcript abundance were validated for a selection of candidate genes using quantitative real-time polymerase chain reaction. This study demonstrates that heterologous microarrays can be successfully employed to study species for which specific microarrays have not yet been developed, and so have the potential to greatly enhance the utility of microarray technology to the field of environmental and functional genomics.

Microarray data classification using automatic SVM kernel selection

Microarray data classification is one of the most important emerging clinical applications in the medical community. Machine learning algorithms are most frequently used to complete this task. We selected one of the state-of-the-art kernel-based algorithms, the support vector machine (SVM), to classify microarray data. As a large number of kernels are available, a significant research question is what is the best kernel for patient diagnosis based on microarray data classification using SVM? We first suggest three solutions based on data visualization and quantitative measures. Different types of microarray problems then test the proposed solutions. Finally, we found that the rule-based approach is most useful for automatic kernel selection for SVM to classify microarray data.

Finding edging genes from microarray data

Motivation: A set of genes and their gene expression levels are used to classify disease and normal tissues. Due to the massive number of genes in microarray, there are a large number of edges to divide different classes of genes in microarray space. The edging genes (EGs) can be co-regulated genes, they can also be on the same pathway or deregulated by the same non-coding genes, such as siRNA or miRNA. Every gene in EGs is vital for identifying a tissue's class. The changing in one EG's gene expression may cause a tissue alteration from normal to disease and vice versa. Finding EGs is of biological importance. In this work, we propose an algorithm to effectively find these EGs.

Result: We tested our algorithm with five microarray datasets. The results are compared with the border-based algorithm which was used to find gene groups and subsequently divide different classes of tissues. Our algorithm finds a significantly larger amount of EGs than does the border-based algorithm. As our algorithm prunes irrelevant patterns at earlier stages, time and space complexities are much less prevalent than in the border-based algorithm.

Microarray classification using statistical learning and decision tree algorithms

This considers the challenging task of cancer prediction based on microarray data for the medical community. The research was conducted on mostly common cancers (breast, colon, long, prostate and leukemia) microarray data analysis, and suggests the use of modern machine learning techniques to predict cancer.

Early breast cancer identification : Which way to go? Microarray or image based computer aided diagnosis!

The goal of this research is to develop a computer aided diagnostic (CAD) system that can detect breast cancer in the early stage by using microarray and image data. We verified the performance of six well known classification algorithms with various performance matrices. Although we do not suggest a unique classifier algorithm for a CAD system, we do identify a number of algorithms whose performance is very promising. The algorithms performance was validated by 3 images dataset; two have been used for the first time in this experiment. Multidimensional image filtering is adopted for the final data extraction. The image data classification performance is compared with microarray data. Results suggest the most effective means of breast cancer identification in the early stage is a hybrid approach.

An agent-based hybrid system for microarray data analysis

This article reports our experience in agent-based hybrid construction for microarray data analysis. The contributions are twofold: We demonstrate that agent-based approaches are suitable for building hybrid systems in general, and that a genetic ensemble system is appropriate for microarray data analysis in particular. Created using an agent-based framework, this genetic ensemble system for microarray data analysis excels in both sample classification accuracy and gene selection reproducibility.

An embedded two-layer feature selection approach for microarray data analysis

Feature selection is an important technique in dealing with application problems with large number of variables and limited training samples, such as image processing, combinatorial chemistry, and microarray analysis. Commonly employed feature selection strategies can be divided into filter and wrapper. In this study, we propose an embedded two-layer feature selection approach to combining the advantages of filter and wrapper algorithms while avoiding their drawbacks. The hybrid algorithm, called GAEF (Genetic Algorithm with embedded filter), divides the feature selection process into two stages. In the first stage, Genetic Algorithm (GA) is employed to pre-select features while in the second stage a filter selector is used to further identify a small feature subset for accurate sample classification. Three benchmark microarray datasets are used to evaluate the proposed algorithm. The experimental results suggest that this embedded two-layer feature selection strategy is able to improve the stability of the selection results as well as the sample classification accuracy.