Clustering Algorithms and Other Exploratory Methods for Microarray Data Analysis

Spotted cDNA microarrays are emerging as a powerful and cost-effective tool for large-scale analysis of gene expression. Microarrays can be used to measure the relative quantities of specific mRNAs in two or more tissue samples for thousands of genes simultaneously. While the power of this technology has been recognized, many open questions remain about appropriate analysis of microarray data. One question is how to make valid estimates of the relative expression for genes that are not biased by ancillary sources of variation. Recognizing that there is inherent "noise" in microarray data, how does one estimate the error variation associated with an estimated change in expression, i.e., how does one construct the error bars? We demonstrate that ANOVA methods can be used to normalize microarray data and provide estimates of changes in gene expression that are corrected for potential confounding effects. This approach establishes a framework for the general analysis and interpretation of microarray data.

The real-time system of the JT-60 has a cascade structure with the major and the minor control loops. The multi-variable feedback control is adopted in the major control loop in order to adjust non-linear effects which will appear in the high-/beta/region. By applying the concept of 'phase shift control' to the control program of the major control loop, a flexible tokamak discharge control is expected to be performed with taking account of machine protection.

cDNA microarrays permit massively parallel gene expression analysis and have spawned a new paradigm in the study of molecular biology. One of the significant challenges in this genomic revolution is to develop sophisticated approaches to facilitate the visualization, analysis, and interpretation of the vast amounts of multi-dimensional gene expression data. We have applied self-organizing map (SOM) in order to meet these challenges. In essence, we utilize U-matrix and component planes in microarray data visualization and introduce general procedure for assessing significance for a cluster detected from U-matrix. Our case studies consist of two data sets. First, we have analyzed a data set containing 13,824 genes in 14 breast cancer cell lines. In the second case we show an example of the SOM in drug treatment of prostate cancer cells. Our results indicate that (1) SOM is capable of helping finding certain biologically meaningful clusters, (2) clustering algorithms could be used for finding a set of potential predictor genes for classification purposes, and (3) comparison and visualization of the effects of different drugs is straightforward with the SOM. In summary, the SOM provides an excellent format for visualization and analysis of gene microarray data, and is likely to facilitate extraction of biologically and medically useful information.

Application of the S-score algorithm for analysis of oligonucleotide microarrays

In the past decade, DNA microarrays have fundamentally changed the way we study complex biological systems. By measuring the expression levels of thousands of transcripts, the paradigm of studying organisms has shifted from focusing on the local phenomena of a few genes to surveying the whole genome. DNA microarrays are used in a variety of ways, from simple comparisons between two samples to more intricate time-series studies. With the large number of genes being studied, the dimensionality of the problem is inevitably high. The analysis of microarray data thus requires specific approaches. In the case of time-series microarray studies, data analysis is further complicated by the correlation between successive time points in a series.In this review, we survey the methodologies used in the analysis of static and time-series microarray data, covering data pre-processing, identification of differentially expressed genes, profile pattern recognition, pathway analysis, and network reconstruction. When available, examples of their use in mammalian cell cultures are presented.

Classification of tumors into subtypes can inform personalized approaches to treatment including the choice of targeted therapies. The two most common lung cancer histological subtypes, lung adenocarcinoma and lung squamous cell carcinoma, have been previously divided into transcriptional subtypes using microarray data, and corresponding signatures were subsequently used to classify RNA-seq data. Cross-platform unsupervised classification facilitates the identification of robust transcriptional subtypes by combining vast amounts of publicly available microarray and RNA-seq data. However, cross-platform classification is challenging because of intrinsic differences in data generated using the two gene expression profiling technologies. In this report, we show that robust gene expression subtypes can be identified in integrated data representing over 3500 normal and tumor lung samples profiled using two widely used platforms, Affymetrix HG-U133 Plus 2.0 Array and Illumina HiSeq RNA sequencing. We tested and analyzed consensus clustering for 384 combinations of data processing methods. The agreement between subtypes identified in single-platform and cross-platform normalized data was then evaluated using a variety of statistics. Results show that unsupervised learning can be achieved with combined microarray and RNA-seq data using selected preprocessing, cross-platform normalization, and unsupervised feature selection methods. Our analysis confirmed three lung adenocarcinoma transcriptional subtypes, but only two consistent subtypes in squamous cell carcinoma, as opposed to four subtypes previously identified. Further analysis showed that tumor subtypes were associated with distinct patterns of genomic alterations in genes coding for therapeutic targets. Importantly, by integrating quantitative proteomics data, we were able to identify tumor subtype biomarkers that effectively classify samples on the basis of both gene and protein expression. This study provides the basis for further integrative data analysis across gene and protein expression profiling platforms.

The purpose of this paper is to introduce transductive inference with support vector machines (TSVM) as a powerful methodology for classification of gene expression data, using training and prediction data sets. The following classification problems will be considered: determination of cancer diagnosis categories and classification of genes from the budding yeast Saccharomyces cerevisiae in functional groups. In the case of training samples, experts have already classified the samples in their respective classes. So, given each prediction sample, the purpose is to determine its corresponding class. The main aspect of TSVM is that the classification task will be implemented in just one step, improving the generalization capability of the classifier. The TSVM will be compared with the traditional inductive method (SVM) in a series of experiments concerning the two classification problems, with promising results.

Development of public toxicogenomics software for microarray data management and analysis

Reproducibility of microarray studies: concordance of current analysis methods

Biological systems can be viewed as information management systems, with a basic instruction set stored in each cell’s DNA as “genes.” For most genes, their information is enabled when they are transcribed into RNA which is subsequently translated into the proteins that form much of a cell’s machinery. Although details of the process for individual genes are known, more complex interactions between elements are yet to be discovered. What we do know is that diseases can result if there are changes in the genes themselves, in the proteins they encode, or if RNAs or proteins are made at the wrong time or in the wrong quantities. Recent advances in biotechnology led to the development of DNA microarrays, which quantitatively measure the expression of thousands of genes simultaneously and provide a snapshot of a cell’s response to a particular condition. Finding patterns of gene expression that provide insight into biological endpoints offers great opportunities for revolutionizing diagnostic and prognostic medicine and providing mechanistic insight in data-driven research in the life sciences, an area with a great need for advances, given the urgency associated with diseases. However, microarray data analysis presents a number of challenges, from noisy data to the curse of dimensionality (large number of features, small number of instances) to problems with no clear solutions (e.g. real world mappings of genes to traits or diseases that are not yet known). Finding patterns of gene expression in microarray data poses problems of class discovery, comparison, prediction, and network analysis which are often approached with AI methods. Many of these methods have been successfully applied to microarray data analysis in a variety of applications ranging from clustering of yeast gene expression patterns (Eisen et al., 1998) to classification of different types of leukemia (Golub et al., 1999). Unsupervised learning methods (e.g. hierarchical clustering) explore clusters in data and have been used for class discovery of distinct forms of diffuse large B-cell lymphoma (Alizadeh et al., 2000). Supervised learning methods (e.g. artificial neural networks) utilize a previously determined mapping between biological samples and classes (i.e. labels) to generate models for class prediction. A k-nearest neighbor (k-NN) approach was used to train a gene expression classifier of different forms of brain tumors and its predictions were able to distinguish biopsy samples with different prognosis suggesting that microarray profiles can predict clinical outcome and direct treatment (Nutt et al., 2003). Bayesian networks constructed from microarray data hold promise for elucidating the underlying biological mechanisms of disease (Friedman et al., 2000).

Biological systems can be viewed as information management systems, with a basic instruction set stored in each cell’s DNA as “genes.” For most genes, their information is enabled when they are transcribed into RNA which is subsequently translated into the proteins that form much of a cell’s machinery. Although details of the process for individual genes are known, more complex interactions between elements are yet to be discovered. What we do know is that diseases can result if there are changes in the genes themselves, in the proteins they encode, or if RNAs or proteins are made at the wrong time or in the wrong quantities. Recent advances in biotechnology led to the development of DNA microarrays, which quantitatively measure the expression of thousands of genes simultaneously and provide a snapshot of a cell’s response to a particular condition. Finding patterns of gene expression that provide insight into biological endpoints offers great opportunities for revolutionizing diagnostic and prognostic medicine and providing mechanistic insight in data-driven research in the life sciences, an area with a great need for advances, given the urgency associated with diseases. However, microarray data analysis presents a number of challenges, from noisy data to the curse of dimensionality (large number of features, small number of instances) to problems with no clear solutions (e.g. real world mappings of genes to traits or diseases that are not yet known). Finding patterns of gene expression in microarray data poses problems of class discovery, comparison, prediction, and network analysis which are often approached with AI methods. Many of these methods have been successfully applied to microarray data analysis in a variety of applications ranging from clustering of yeast gene expression patterns (Eisen et al., 1998) to classification of different types of leukemia (Golub et al., 1999). Unsupervised learning methods (e.g. hierarchical clustering) explore clusters in data and have been used for class discovery of distinct forms of diffuse large B-cell lymphoma (Alizadeh et al., 2000). Supervised learning methods (e.g. artificial neural networks) utilize a previously determined mapping between biological samples and classes (i.e. labels) to generate models for class prediction. A k-nearest neighbor (k-NN) approach was used to train a gene expression classifier of different forms of brain tumors and its predictions were able to distinguish biopsy samples with different prognosis suggesting that microarray profiles can predict clinical outcome and direct treatment (Nutt et al., 2003). Bayesian networks constructed from microarray data hold promise for elucidating the underlying biological mechanisms of disease (Friedman et al., 2000). Request access from your librarian to read this chapter's full text.

Transcription factors (TFs) are responsible for regulating the temporal and tissue specific expression of the genome. Identifying the complete battery of genes that are targeted by individual TFs, how these target genes interact within a cellular network, and the role these networks play in various disease states is essential to pharmacology and toxicology research. Genomic tools have been and are being developed to address these issues on a global scale. The most widely used tool among them is the microarray. cDNA and oligonucleotide arrays have become standard tools to study TFs and identify regulatory networks. Understanding microarray data requires careful attention to experimental design, platforms, model systems and data analysis. Microarray data analysis has also become increasingly complex with the use of various error models and clustering algorithms. Finally, new in silico approaches have been utilized to further characterize TF signaling networks. These approaches utilize computer based modeling, chromatin immunoprecipitation and microarray experiments. The application of these approaches and some concerns with the various approaches and their application to TF research are discussed.

Dimension reduction is an important issue to understand microarray data. In this study, we proposed a efficient approach for dimensionality reduction of microarray data. Our method allows to apply the manifold learning algorithm to analyses dimensionality reduction of microarray data. The intra-/inter-category distances were used as the criteria to quantitatively evaluate the effects of data dimensionality reduction. Colon cancer and leukaemia gene expression datasets are selected for our investigation. When the neighborhood parameter was effectivly set, all the intrinsic dimension numbers of data sets were low. Therefore, manifold learning is used to study microarray data in the low-dimensional projection space. Our results indicate that Manifold learning method possesses better effects than the linear methods in analysis of microarray data, which is suitable for clinical diagnosis and other medical applications.

Unsupervised learning from EEG data for epilepsy: A systematic literature review.

Computational analysis methods including machine learning have a significant impact in the fields of genomics and medicine. High-throughput gene expression analysis methods such as microarray technology and RNA sequencing produce enormous amounts of data. Traditionally, statistical methods are used for comparative analysis of gene expression data. However, more complex analysis for classification of sample observations, or discovery of feature genes requires sophisticated computational approaches. In this review, we compile various statistical and computational tools used in analysis of expression microarray data. Even though the methods are discussed in the context of expression microarrays, they can also be applied for the analysis of RNA sequencing and quantitative proteomics datasets. We discuss the types of missing values, and the methods and approaches usually employed in their imputation. We also discuss methods of data normalization, feature selection, and feature extraction. Lastly, methods of classification and class discovery along with their evaluation parameters are described in detail. We believe that this detailed review will help the users to select appropriate methods for preprocessing and analysis of their data based on the expected outcome.