Search results for: microarray datasets

Authors: R. K. Agrawal, Rajni Bala

Abstract:

Developing an accurate classifier for high dimensional microarray datasets is a challenging task due to availability of small sample size. Therefore, it is important to determine a set of relevant genes that classify the data well. Traditionally, gene selection method often selects the top ranked genes according to their discriminatory power. Often these genes are correlated with each other resulting in redundancy. In this paper, we have proposed a hybrid method using feature ranking and wrapper method (Genetic Algorithm with multiclass SVM) to identify a set of relevant genes that classify the data more accurately. A new fitness function for genetic algorithm is defined that focuses on selecting the smallest set of genes that provides maximum accuracy. Experiments have been carried on four well-known datasets1. The proposed method provides better results in comparison to the results found in the literature in terms of both classification accuracy and number of genes selected.

Keywords: Gene selection, genetic algorithm, microarray datasets, multi-class SVM.

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Authors: R. Mallika, V. Saravanan

Abstract:

This paper gives a novel method for improving classification performance for cancer classification with very few microarray Gene expression data. The method employs classification with individual gene ranking and gene subset ranking. For selection and classification, the proposed method uses the same classifier. The method is applied to three publicly available cancer gene expression datasets from Lymphoma, Liver and Leukaemia datasets. Three different classifiers namely Support vector machines-one against all (SVM-OAA), K nearest neighbour (KNN) and Linear Discriminant analysis (LDA) were tested and the results indicate the improvement in performance of SVM-OAA classifier with satisfactory results on all the three datasets when compared with the other two classifiers.

Keywords: Support vector machines-one against all, cancerclassification, Linear Discriminant analysis, K nearest neighbour, microarray gene expression, gene pair ranking.

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Authors: Younies Mahmoud, Mai Mabrouk, Elsayed Sallam

Abstract:

Analyzing DNA microarray data sets is a great challenge, which faces the bioinformaticians due to the complication of using statistical and machine learning techniques. The challenge will be doubled if the microarray data sets contain missing data, which happens regularly because these techniques cannot deal with missing data. One of the most important data analysis process on the microarray data set is feature selection. This process finds the most important genes that affect certain disease. In this paper, we introduce a technique for imputing the missing data in microarray data sets while performing feature selection.

Keywords: DNA microarray, feature selection, missing data, bioinformatics.

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Authors: Seo Young Kim, Tai Myong Choi

Abstract:

The main goal of microarray experiments is to quantify the expression of every object on a slide as precisely as possible, with a further goal of clustering the objects. Recently, many studies have discussed clustering issues involving similar patterns of gene expression. This paper presents an application of fuzzy-type methods for clustering DNA microarray data that can be applied to typical comparisons. Clustering and analyses were performed on microarray and simulated data. The results show that fuzzy-possibility c-means clustering substantially improves the findings obtained by others.

Keywords: Clustering, microarray data, Fuzzy-type clustering, Validation

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Authors: C. Gunavathi, K. Premalatha

Abstract:

Tumor classification is a key area of research in the field of bioinformatics. Microarray technology is commonly used in the study of disease diagnosis using gene expression levels. The main drawback of gene expression data is that it contains thousands of genes and a very few samples. Feature selection methods are used to select the informative genes from the microarray. These methods considerably improve the classification accuracy. In the proposed method, Genetic Algorithm (GA) is used for effective feature selection. Informative genes are identified based on the T-Statistics, Signal-to-Noise Ratio (SNR) and F-Test values. The initial candidate solutions of GA are obtained from top-m informative genes. The classification accuracy of k-Nearest Neighbor (kNN) method is used as the fitness function for GA. In this work, kNN and Support Vector Machine (SVM) are used as the classifiers. The experimental results show that the proposed work is suitable for effective feature selection. With the help of the selected genes, GA-kNN method achieves 100% accuracy in 4 datasets and GA-SVM method achieves in 5 out of 10 datasets. The GA with kNN and SVM methods are demonstrated to be an accurate method for microarray based tumor classification.

Keywords: F-Test, Gene Expression, Genetic Algorithm, k- Nearest-Neighbor, Microarray, Signal-to-Noise Ratio, Support Vector Machine, T-statistics, Tumor Classification.

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Authors: M. Pandi, K. Premalatha

Abstract:

A DNA microarray technology is a collection of microscopic DNA spots attached to a solid surface. Scientists use DNA microarrays to measure the expression levels of large numbers of genes simultaneously or to genotype multiple regions of a genome. Elucidating the patterns hidden in gene expression data offers a tremendous opportunity for an enhanced understanding of functional genomics. However, the large number of genes and the complexity of biological networks greatly increase the challenges of comprehending and interpreting the resulting mass of data, which often consists of millions of measurements. It is handled by clustering which reveals the natural structures and identifying the interesting patterns in the underlying data. In this paper, gene based clustering in gene expression data is proposed using Cuckoo Search with Differential Evolution (CS-DE). The experiment results are analyzed with gene expression benchmark datasets. The results show that CS-DE outperforms CS in benchmark datasets. To find the validation of the clustering results, this work is tested with one internal and one external cluster validation indexes.

Keywords: DNA, Microarray, genomics, Cuckoo Search, Differential Evolution, Gene expression data, Clustering.

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Authors: C. Gunavathi, K. Premalatha

Abstract:

Microarray technology is universally used in the study of disease diagnosis using gene expression levels. The main shortcoming of gene expression data is that it includes thousands of genes and a small number of samples. Abundant methods and techniques have been proposed for tumor classification using microarray gene expression data. Feature or gene selection methods can be used to mine the genes that directly involve in the classification and to eliminate irrelevant genes. In this paper statistical measures like T-Statistics, Signal-to-Noise Ratio (SNR) and F-Statistics are used to rank the genes. The ranked genes are used for further classification. Particle Swarm Optimization (PSO) algorithm and Shuffled Frog Leaping (SFL) algorithm are used to find the significant genes from the top-m ranked genes. The Naïve Bayes Classifier (NBC) is used to classify the samples based on the significant genes. The proposed work is applied on Lung and Ovarian datasets. The experimental results show that the proposed method achieves 100% accuracy in all the three datasets and the results are compared with previous works.

Keywords: Microarray, T-Statistics, Signal-to-Noise Ratio, FStatistics, Particle Swarm Optimization, Shuffled Frog Leaping, Naïve Bayes Classifier.

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Authors: Chieh-Yuan Tsai, Chuang-Cheng Chiu

Abstract:

Biclustering aims at identifying several biclusters that reveal potential local patterns from a microarray matrix. A bicluster is a sub-matrix of the microarray consisting of only a subset of genes co-regulates in a subset of conditions. In this study, we extend the motif of subspace clustering to present a K-biclusters clustering (KBC) algorithm for the microarray biclustering issue. Besides minimizing the dissimilarities between genes and bicluster centers within all biclusters, the objective function of the KBC algorithm additionally takes into account how to minimize the residues within all biclusters based on the mean square residue model. In addition, the objective function also maximizes the entropy of conditions to stimulate more conditions to contribute the identification of biclusters. The KBC algorithm adopts the K-means type clustering process to efficiently make the partition of K biclusters be optimized. A set of experiments on a practical microarray dataset are demonstrated to show the performance of the proposed KBC algorithm.

Keywords: Microarray, Biclustering, Subspace clustering, Meansquare residue model.

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Authors: Dong Hoon Lim

Abstract:

A series of microarray experiments produces observations of differential expression for thousands of genes across multiple conditions. Principal component analysis(PCA) has been widely used in multivariate data analysis to reduce the dimensionality of the data in order to simplify subsequent analysis and allow for summarization of the data in a parsimonious manner. PCA, which can be implemented via a singular value decomposition(SVD), is useful for analysis of microarray data. For application of PCA using SVD we use the DNA microarray data for the small round blue cell tumors(SRBCT) of childhood by Khan et al.(2001). To decide the number of components which account for sufficient amount of information we draw scree plot. Biplot, a graphic display associated with PCA, reveals important features that exhibit relationship between variables and also the relationship of variables with observations.

Keywords: Principal component analysis, singular value decomposition, microarray data, SRBCT

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Authors: Rameswar Debnath, Haruhisa Takahashi

Abstract:

An evolutionary method whose selection and recombination operations are based on generalization error-bounds of support vector machine (SVM) can select a subset of potentially informative genes for SVM classifier very efficiently [7]. In this paper, we will use the derivative of error-bound (first-order criteria) to select and recombine gene features in the evolutionary process, and compare the performance of the derivative of error-bound with the error-bound itself (zero-order) in the evolutionary process. We also investigate several error-bounds and their derivatives to compare the performance, and find the best criteria for gene selection and classification. We use 7 cancer-related human gene expression datasets to evaluate the performance of the zero-order and first-order criteria of error-bounds. Though both criteria have the same strategy in theoretically, experimental results demonstrate the best criterion for microarray gene expression data.

Keywords: support vector machine, generalization error-bound, feature selection, evolutionary algorithm, microarray data

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Authors: Alexandra Oliveros, Miguel Sotaquirá

Abstract:

DNA microarray technology is widely used by geneticists to diagnose or treat diseases through gene expression. This technology is based on the hybridization of a tissue-s DNA sequence into a substrate and the further analysis of the image formed by the thousands of genes in the DNA as green, red or yellow spots. The process of DNA microarray image analysis involves finding the location of the spots and the quantification of the expression level of these. In this paper, a tool to perform DNA microarray image analysis is presented, including a spot addressing method based on the image projections, the spot segmentation through contour based segmentation and the extraction of relevant information due to gene expression.

Keywords: Contour segmentation, DNA microarrays, edge detection, image processing, segmentation, spot addressing.

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Authors: Fabian Horn, Reinhard Guthke

Abstract:

In molecular biology, microarray technology is widely and successfully utilized to efficiently measure gene activity. If working with less studied organisms, methods to design custom-made microarray probes are available. One design criterion is to select probes with minimal melting temperature variances thus ensuring similar hybridization properties. If the microarray application focuses on the investigation of metabolic pathways, it is not necessary to cover the whole genome. It is more efficient to cover each metabolic pathway with a limited number of genes. Firstly, an approach is presented which minimizes the overall melting temperature variance of selected probes for all genes of interest. Secondly, the approach is extended to include the additional constraints of covering all pathways with a limited number of genes while minimizing the overall variance. The new optimization problem is solved by a bottom-up programming approach which reduces the complexity to make it computationally feasible. The new method is exemplary applied for the selection of microarray probes in order to cover all fungal secondary metabolite gene clusters for Aspergillus terreus.

Keywords: bottom-up approach, gene clusters, melting temperature, metabolic pathway, microarray probe design, probe selection

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Authors: Frank Emmert Streib, Matthias Dehmer, Gökhan H. Bakır, Max Mühlhauser

Abstract:

In this paper we investigate the influence of external noise on the inference of network structures. The purpose of our simulations is to gain insights in the experimental design of microarray experiments to infer, e.g., transcription regulatory networks from microarray experiments. Here external noise means, that the dynamics of the system under investigation, e.g., temporal changes of mRNA concentration, is affected by measurement errors. Additionally to external noise another problem occurs in the context of microarray experiments. Practically, it is not possible to monitor the mRNA concentration over an arbitrary long time period as demanded by the statistical methods used to learn the underlying network structure. For this reason, we use only short time series to make our simulations more biologically plausible.

Keywords: Dynamic Bayesian networks, structure learning, gene networks, Markov chain Monte Carlo, microarray data.

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Authors: Seo Young Kim, Jae Won Lee, Jong Sung Bae

Abstract:

Microarray experiments are information rich; however, extensive data mining is required to identify the patterns that characterize the underlying mechanisms of action. For biologists, a key aim when analyzing microarray data is to group genes based on the temporal patterns of their expression levels. In this paper, we used an iterative clustering method to find temporal patterns of gene expression. We evaluated the performance of this method by applying it to real sporulation data and simulated data. The patterns obtained using the iterative clustering were found to be superior to those obtained using existing clustering algorithms.

Keywords: Clustering, microarray experiment, temporal pattern of gene expression data.

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Authors: Mona Heydari, Ehsan Motamedian, Seyed Abbas Shojaosadati

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Prediction of perturbations after genetic manipulation (especially gene knockout) is one of the important challenges in systems biology. In this paper, a new algorithm is introduced that integrates microarray data into the metabolic model. The algorithm was used to study the change in the cell phenotype after knockout of Gss gene in Escherichia coli BW25113. Algorithm implementation indicated that gene deletion resulted in more activation of the metabolic network. Growth yield was more and less regulating gene were identified for mutant in comparison with the wild-type strain.

Keywords: Metabolic network, gene knockout, flux balance analysis, microarray data, integration.

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Authors: Rio G. L. D'Souza, K. Chandra Sekaran, A. Kandasamy

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.

Keywords: Evolutionary computing, gene expression analysis, gene networks, microarray data analysis, phenomic algorithms.

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Authors: Frank Emmert Streib, Matthias Dehmer, Jing Liu, Max Mühlhauser

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In this paper we present a method for gene ranking from DNA microarray data. More precisely, we calculate the correlation networks, which are unweighted and undirected graphs, from microarray data of cervical cancer whereas each network represents a tissue of a certain tumor stage and each node in the network represents a gene. From these networks we extract one tree for each gene by a local decomposition of the correlation network. The interpretation of a tree is that it represents the n-nearest neighbor genes on the n-th level of a tree, measured by the Dijkstra distance, and, hence, gives the local embedding of a gene within the correlation network. For the obtained trees we measure the pairwise similarity between trees rooted by the same gene from normal to cancerous tissues. This evaluates the modification of the tree topology due to progression of the tumor. Finally, we rank the obtained similarity values from all tissue comparisons and select the top ranked genes. For these genes the local neighborhood in the correlation networks changes most between normal and cancerous tissues. As a result we find that the top ranked genes are candidates suspected to be involved in tumor growth and, hence, indicates that our method captures essential information from the underlying DNA microarray data of cervical cancer.

Keywords: Graph similarity, DNA microarray data, cancer.

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Authors: R. Balamurugan, A. M. Natarajan, K. Premalatha

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Microarray gene expression data play a vital in biological processes, gene regulation and disease mechanism. Biclustering in gene expression data is a subset of the genes indicating consistent patterns under the subset of the conditions. Finding a biclustering is an optimization problem. In recent years, swarm intelligence techniques are popular due to the fact that many real-world problems are increasingly large, complex and dynamic. By reasons of the size and complexity of the problems, it is necessary to find an optimization technique whose efficiency is measured by finding the near optimal solution within a reasonable amount of time. In this paper, the algorithmic concepts of the Particle Swarm Optimization (PSO), Shuffled Frog Leaping (SFL) and Cuckoo Search (CS) algorithms have been analyzed for the four benchmark gene expression dataset. The experiment results show that CS outperforms PSO and SFL for 3 datasets and SFL give better performance in one dataset. Also this work determines the biological relevance of the biclusters with Gene Ontology in terms of function, process and component.

Keywords: Particle swarm optimization, Shuffled frog leaping, Cuckoo search, biclustering, gene expression data.

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Authors: Frank Emmert-Streib, Matthias Dehmer, Jing Liu, Max Muhlhauser

Abstract:

The major objective of this paper is to introduce a new method to select genes from DNA microarray data. As criterion to select genes we suggest to measure the local changes in the correlation graph of each gene and to select those genes whose local changes are largest. More precisely, we calculate the correlation networks from DNA microarray data of cervical cancer whereas each network represents a tissue of a certain tumor stage and each node in the network represents a gene. From these networks we extract one tree for each gene by a local decomposition of the correlation network. The interpretation of a tree is that it represents the n-nearest neighbor genes on the n-th level of a tree, measured by the Dijkstra distance, and, hence, gives the local embedding of a gene within the correlation network. For the obtained trees we measure the pairwise similarity between trees rooted by the same gene from normal to cancerous tissues. This evaluates the modification of the tree topology due to tumor progression. Finally, we rank the obtained similarity values from all tissue comparisons and select the top ranked genes. For these genes the local neighborhood in the correlation networks changes most between normal and cancerous tissues. As a result we find that the top ranked genes are candidates suspected to be involved in tumor growth. This indicates that our method captures essential information from the underlying DNA microarray data of cervical cancer.

Keywords: Graph similarity, generalized trees, graph alignment, DNA microarray data, cervical cancer.

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Authors: Mario Mastriani

Abstract:

We describe a novel method for removing noise (in wavelet domain) of unknown variance from microarrays. The method is based on the following procedure: We apply 1) Bidimentional Discrete Wavelet Transform (DWT-2D) to the Noisy Microarray, 2) scaling and rounding to the coefficients of the highest subbands (to obtain integer and positive coefficients), 3) bit-slicing to the new highest subbands (to obtain bit-planes), 4) then we apply the Systholic Boolean Orthonormalizer Network (SBON) to the input bit-plane set and we obtain two orthonormal otput bit-plane sets (in a Boolean sense), we project a set on the other one, by means of an AND operation, and then, 5) we apply re-assembling, and, 6) rescaling. Finally, 7) we apply Inverse DWT-2D and reconstruct a microarray from the modified wavelet coefficients. Denoising results compare favorably to the most of methods in use at the moment.

Keywords: Bit-Plane, Boolean Orthonormalization Process, Denoising, Microarrays, Wavelets

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Authors: Mario Mastriani, Alberto E. Giraldez

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We describe a novel method for removing noise (in wavelet domain) of unknown variance from microarrays. The method is based on a smoothing of the coefficients of the highest subbands. Specifically, we decompose the noisy microarray into wavelet subbands, apply smoothing within each highest subband, and reconstruct a microarray from the modified wavelet coefficients. This process is applied a single time, and exclusively to the first level of decomposition, i.e., in most of the cases, it is not necessary a multirresoltuion analysis. Denoising results compare favorably to the most of methods in use at the moment.

Keywords: Directional smoothing, denoising, edge preservation, microarrays, thresholding, wavelets

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Authors: Ghada A. Alfattni

Abstract:

Analysing unbalanced datasets is one of the challenges that practitioners in machine learning field face. However, many researches have been carried out to determine the effectiveness of the use of the synthetic minority over-sampling technique (SMOTE) to address this issue. The aim of this study was therefore to compare the effectiveness of the SMOTE over different models on unbalanced datasets. Three classification models (Logistic Regression, Support Vector Machine and Nearest Neighbour) were tested with multiple datasets, then the same datasets were oversampled by using SMOTE and applied again to the three models to compare the differences in the performances. Results of experiments show that the highest number of nearest neighbours gives lower values of error rates. 

Keywords: Imbalanced datasets, SMOTE, machine learning, logistic regression, support vector machine, nearest neighbour.

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Authors: Ali Anaissi, Paul J. Kennedy, Madhu Goyal

Abstract:

Analysis and visualization of microarraydata is veryassistantfor biologists and clinicians in the field of diagnosis and treatment of patients. It allows Clinicians to better understand the structure of microarray and facilitates understanding gene expression in cells. However, microarray dataset is a complex data set and has thousands of features and a very small number of observations. This very high dimensional data set often contains some noise, non-useful information and a small number of relevant features for disease or genotype. This paper proposes a non-linear dimensionality reduction algorithm Local Principal Component (LPC) which aims to maps high dimensional data to a lower dimensional space. The reduced data represents the most important variables underlying the original data. Experimental results and comparisons are presented to show the quality of the proposed algorithm. Moreover, experiments also show how this algorithm reduces high dimensional data whilst preserving the neighbourhoods of the points in the low dimensional space as in the high dimensional space.

Keywords: Linear Dimension Reduction, Non-Linear Dimension Reduction, Principal Component Analysis, Biologists.

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Authors: Aboamama Atahar Ahmed, Muhammad Shafie Abd Latiff, Kamalrulnizam Abu Bakar, Zainul AhmadRajion

Abstract:

Distance visualization of large datasets often takes the direction of remote viewing and zooming techniques of stored static images. However, the continuous increase in the size of datasets and visualization operation causes insufficient performance with traditional desktop computers. Additionally, the visualization techniques such as Isosurface depend on the available resources of the running machine and the size of datasets. Moreover, the continuous demand for powerful computing powers and continuous increase in the size of datasets results an urgent need for a grid computing infrastructure. However, some issues arise in current grid such as resources availability at the client machines which are not sufficient enough to process large datasets. On top of that, different output devices and different network bandwidth between the visualization pipeline components often result output suitable for one machine and not suitable for another. In this paper we investigate how the grid services could be used to support remote visualization of large datasets and to break the constraint of physical co-location of the resources by applying the grid computing technologies. We show our grid enabled architecture to visualize large medical datasets (circa 5 million polygons) for remote interactive visualization on modest resources clients.

Keywords: Visualization, Grid computing, Medical datasets, visualization techniques, thin clients, Globus toolkit, VTK.

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Authors: U. Kairov, T. Karpenyuk, E. Ramanculov, A. Zinovyev

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The most common result of analysis of highthroughput data in molecular biology represents a global list of genes, ranked accordingly to a certain score. The score can be a measure of differential expression. Recent work proposed a new method for selecting a number of genes in a ranked gene list from microarray gene expression data such that this set forms the Optimally Functionally Enriched Network (OFTEN), formed by known physical interactions between genes or their products. Here we present calculation results of relative connectivity of genes from META-OFTEN network and tentative biological interpretation of the most reproducible signal. The relative connectivity and inbetweenness values of genes from META-OFTEN network were estimated.

Keywords: Microarray, META-OFTEN, gene network.

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Authors: Mehmet Hacibeyoglu, Ahmet Arslan, Sirzat Kahramanli

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This study analyzes the effect of discretization on classification of datasets including continuous valued features. Six datasets from UCI which containing continuous valued features are discretized with entropy-based discretization method. The performance improvement between the dataset with original features and the dataset with discretized features is compared with k-nearest neighbors, Naive Bayes, C4.5 and CN2 data mining classification algorithms. As the result the classification accuracies of the six datasets are improved averagely by 1.71% to 12.31%.

Keywords: Data mining classification algorithms, entropy-baseddiscretization method

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Authors: Chintanu K. Sarmah, Sandhya Samarasinghe, Don Kulasiri, Daniel Catchpoole

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Gene expression profiling is rapidly evolving into a powerful technique for investigating tumor malignancies. The researchers are overwhelmed with the microarray-based platforms and methods that confer them the freedom to conduct large-scale gene expression profiling measurements. Simultaneously, investigations into cross-platform integration methods have started gaining momentum due to their underlying potential to help comprehend a myriad of broad biological issues in tumor diagnosis, prognosis, and therapy. However, comparing results from different platforms remains to be a challenging task as various inherent technical differences exist between the microarray platforms. In this paper, we explain a simple ratio-transformation method, which can provide some common ground for cDNA and Affymetrix platform towards cross-platform integration. The method is based on the characteristic data attributes of Affymetrix- and cDNA- platform. In the work, we considered seven childhood leukemia patients and their gene expression levels in either platform. With a dataset of 822 differentially expressed genes from both these platforms, we carried out a specific ratio-treatment to Affymetrix data, which subsequently showed an improvement in the relationship with the cDNA data.

Keywords: Gene expression profiling, microarray, cDNA, Affymetrix, childhood leukaemia.

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Authors: M. Anandhavalli Gauthaman

Abstract:

DNA microarrays allow the measurement of expression levels for a large number of genes, perhaps all genes of an organism, within a number of different experimental samples. It is very much important to extract biologically meaningful information from this huge amount of expression data to know the current state of the cell because most cellular processes are regulated by changes in gene expression. Association rule mining techniques are helpful to find association relationship between genes. Numerous association rule mining algorithms have been developed to analyze and associate this huge amount of gene expression data. This paper focuses on some of the popular association rule mining algorithms developed to analyze gene expression data.

Keywords: DNA microarray, gene expression, association rule mining.

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Authors: Moez Ben Hadj Hamida, Yahya SlimaniI

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In this paper, we propose an adaptation of the Patricia-Tree for sparse datasets to generate non redundant rule associations. Using this adaptation, we can generate frequent closed itemsets that are more compact than frequent itemsets used in Apriori approach. This adaptation has been experimented on a set of datasets benchmarks.

Keywords: Datamining, Frequent itemsets, Frequent closeditemsets, Sparse datasets.

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Authors: Seo Young Kim, Toshimitsu Hamasaki

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.

Keywords: Gene expression, clustering, data preprocessing.

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