Abstract: Development of a method to estimate gene functions is
an important task in bioinformatics. One of the approaches for the
annotation is the identification of the metabolic pathway that genes are
involved in. Since gene expression data reflect various intracellular
phenomena, those data are considered to be related with genes’
functions. However, it has been difficult to estimate the gene function
with high accuracy. It is considered that the low accuracy of the
estimation is caused by the difficulty of accurately measuring a gene
expression. Even though they are measured under the same condition,
the gene expressions will vary usually. In this study, we proposed a
feature extraction method focusing on the variability of gene
expressions to estimate the genes' metabolic pathway accurately. First,
we estimated the distribution of each gene expression from replicate
data. Next, we calculated the similarity between all gene pairs by KL
divergence, which is a method for calculating the similarity between
distributions. Finally, we utilized the similarity vectors as feature
vectors and trained the multiclass SVM for identifying the genes'
metabolic pathway. To evaluate our developed method, we applied the
method to budding yeast and trained the multiclass SVM for
identifying the seven metabolic pathways. As a result, the accuracy
that calculated by our developed method was higher than the one that
calculated from the raw gene expression data. Thus, our developed
method combined with KL divergence is useful for identifying the
genes' metabolic pathway.
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.
Abstract: 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.
Abstract: Microarrays are made it possible to simultaneously monitor the expression profiles of thousands of genes under various experimental conditions. It is used to identify the co-expressed genes in specific cells or tissues that are actively used to make proteins. This method is used to analysis the gene expression, an important task in bioinformatics research. Cluster analysis of gene expression data has proved to be a useful tool for identifying co-expressed genes, biologically relevant groupings of genes and samples. In this work K-Means algorithms has been applied for clustering of Gene Expression Data. Further, rough set based Quick reduct algorithm has been applied for each cluster in order to select the most similar genes having high correlation. Then the ACV measure is used to evaluate the refined clusters and classification is used to evaluate the proposed method. They could identify compact clusters with feature selection method used to genes are selected.
Abstract: Feature selection is a process to select features which are more informative. It is one of the important steps in knowledge discovery. The problem is that all genes are not important in gene expression data. Some of the genes may be redundant, and others may be irrelevant and noisy. Here a novel approach is proposed Hybrid K-Mean-Quick Reduct (KMQR) algorithm for gene selection from gene expression data. In this study, the entire dataset is divided into clusters by applying K-Means algorithm. Each cluster contains similar genes. The high class discriminated genes has been selected based on their degree of dependence by applying Quick Reduct algorithm to all the clusters. Average Correlation Value (ACV) is calculated for the high class discriminated genes. The clusters which have the ACV value as 1 is determined as significant clusters, whose classification accuracy will be equal or high when comparing to the accuracy of the entire dataset. The proposed algorithm is evaluated using WEKA classifiers and compared. The proposed work shows that the high classification accuracy.
Abstract: Reverse engineering of genetic regulatory network involves the modeling of the given gene expression data into a form of the network. Computationally it is possible to have the relationships between genes, so called gene regulatory networks (GRNs), that can help to find the genomics and proteomics based diagnostic approach for any disease. In this paper, clustering based method has been used to reconstruct genetic regulatory network from time series gene expression data. Supercoiled data set from Escherichia coli has been taken to demonstrate the proposed method.
Abstract: The DNA microarray technology concurrently monitors the expression levels of thousands of genes during significant biological processes and across the related samples. The better understanding of functional genomics is obtained by extracting the patterns hidden in gene expression data. It is handled by clustering which reveals natural structures and identify interesting patterns in the underlying data. In the proposed work clustering gene expression data is done through an Advanced Nelder Mead (ANM) algorithm. Nelder Mead (NM) method is a method designed for optimization process. In Nelder Mead method, the vertices of a triangle are considered as the solutions. Many operations are performed on this triangle to obtain a better result. In the proposed work, the operations like reflection and expansion is eliminated and a new operation called spread-out is introduced. The spread-out operation will increase the global search area and thus provides a better result on optimization. The spread-out operation will give three points and the best among these three points will be used to replace the worst point. The experiment results are analyzed with optimization benchmark test functions and gene expression benchmark datasets. The results show that ANM outperforms NM in both benchmarks.
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: 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.
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.
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.
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.