New Spiked-In Probe Sets for the Affymetrix HGU-133A Latin Square Experiment

The Affymetrix HGU-133A spike in data set has been used for determining the sensitivity and specificity of various methods for the analysis of microarray data. We show that there are 22 additional probe sets that detect spike in RNAs that should be considered as spike in probe sets. We assign each proposed spiked-in probe set to a concentration group within the Latin Square design, and examine the effects of the additional spiked-in probe sets on assessing the accuracy of analysis methods currently in use. We show that several popular preprocessing methods are more sensitive and specific when the new spike-ins are used to determine false positive and false negative rates

A Method to Detect AAC Audio Forgery

Advanced Audio Coding (AAC), a standardized lossy compression scheme for digital audio, which was designed to be the successor of the MP3 format, generally achieves better sound quality than MP3 at similar bit rates. While AAC is also the default or standard audio format for many devices and AAC audio files may be presented as important digital evidences, the authentication of the audio files is highly needed but relatively missing. In this paper, we propose a scheme to expose tampered AAC audio streams that are encoded at the same encoding bit-rate. Specifically, we design a shift-recompression based method to retrieve the differential features between the re-encoded audio stream at each shifting and original audio stream, learning classifier is employed to recognize different patterns of differential features of the doctored forgery files and original (untouched) audio files. Experimental results show that our approach is very promising and effective to detect the forgery of the same encoding bit-rate on AAC audio streams. Our study also shows that shift recompression-based differential analysis is very effective for detection of the MP3 forgery at the same bit rate

A distribution-free convolution model for background correction of oligonucleotide microarray data

IntroductionAffymetrix GeneChip® high-density oligonucleotide arrays are widely used in biological and medical research because of production reproducibility, which facilitates the comparison of results between experiment runs. In order to obtain high-level classification and cluster analysis that can be trusted, it is important to perform various pre-processing steps on the probe-level data to control for variability in sample processing and array hybridization. Many proposed preprocessing methods are parametric, in that they assume that the background noise generated by microarray data is a random sample from a statistical distribution, typically a normal distribution. The quality of the final results depends on the validity of such assumptions. ResultsWe propose a Distribution Free Convolution Model (DFCM) to circumvent observed deficiencies in meeting and validating distribution assumptions of parametric methods. Knowledge of array structure and the biological function of the probes indicate that the intensities of mismatched (MM) probes that correspond to the smallest perfect match (PM) intensities can be used to estimate the background noise. Specifically, we obtain the smallest q2 percent of the MM intensities that are associated with the lowest q1 percent PM intensities, and use these intensities to estimate background. ConclusionUsing the Affymetrix Latin Square spike-in experiments, we show that the background noise generated by microarray experiments typically is not well modeled by a single overall normal distribution. We further show that the signal is not exponentially distributed, as is also commonly assumed. Therefore, DFCM has better sensitivity and specificity, as measured by ROC curves and area under the curve (AUC) than MAS 5.0, RMA, RMA with no background correction (RMA-noBG), GCRMA, PLIER, and dChip (MBEI) for preprocessing of Affymetrix microarray data. These results hold for two spike-in data sets and one real data set that were analyzed. Comparisons with other methods on two spike-in data sets and one real data set show that our nonparametric methods are a superior alternative for background correction of Affymetrix data

A gene selection method for GeneChip array data with small sample sizes

<p>Abstract</p> <p>Background</p> <p>In microarray experiments with small sample sizes, it is a challenge to estimate p-values accurately and decide cutoff p-values for gene selection appropriately. Although permutation-based methods have proved to have greater sensitivity and specificity than the regular t-test, their p-values are highly discrete due to the limited number of permutations available in very small sample sizes. Furthermore, estimated permutation-based p-values for true nulls are highly correlated and not uniformly distributed between zero and one, making it difficult to use current false discovery rate (FDR)-controlling methods.</p> <p>Results</p> <p>We propose a model-based information sharing method (MBIS) that, after an appropriate data transformation, utilizes information shared among genes. We use a normal distribution to model the mean differences of true nulls across two experimental conditions. The parameters of the model are then estimated using all data in hand. Based on this model, p-values, which are uniformly distributed from true nulls, are calculated. Then, since FDR-controlling methods are generally not well suited to microarray data with very small sample sizes, we select genes for a given cutoff p-value and then estimate the false discovery rate.</p> <p>Conclusion</p> <p>Simulation studies and analysis using real microarray data show that the proposed method, MBIS, is more powerful and reliable than current methods. It has wide application to a variety of situations.</p

Feature Selection and Classification of MAQC-II Breast Cancer and Multiple Myeloma Microarray Gene Expression Data

Microarray data has a high dimension of variables but available datasets usually have only a small number of samples, thereby making the study of such datasets interesting and challenging. In the task of analyzing microarray data for the purpose of, e.g., predicting gene-disease association, feature selection is very important because it provides a way to handle the high dimensionality by exploiting information redundancy induced by associations among genetic markers. Judicious feature selection in microarray data analysis can result in significant reduction of cost while maintaining or improving the classification or prediction accuracy of learning machines that are employed to sort out the datasets. In this paper, we propose a gene selection method called Recursive Feature Addition (RFA), which combines supervised learning and statistical similarity measures. We compare our method with the following gene selection methods

Gene selection and classification for cancer microarray data based on machine learning and similarity measures

<p>Abstract</p> <p>Background</p> <p>Microarray data have a high dimension of variables and a small sample size. In microarray data analyses, two important issues are how to choose genes, which provide reliable and good prediction for disease status, and how to determine the final gene set that is best for classification. Associations among genetic markers mean one can exploit information redundancy to potentially reduce classification cost in terms of time and money.</p> <p>Results</p> <p>To deal with redundant information and improve classification, we propose a gene selection method, Recursive Feature Addition, which combines supervised learning and statistical similarity measures. To determine the final optimal gene set for prediction and classification, we propose an algorithm, Lagging Prediction Peephole Optimization. By using six benchmark microarray gene expression data sets, we compared Recursive Feature Addition with recently developed gene selection methods: Support Vector Machine Recursive Feature Elimination, Leave-One-Out Calculation Sequential Forward Selection and several others.</p> <p>Conclusions</p> <p>On average, with the use of popular learning machines including Nearest Mean Scaled Classifier, Support Vector Machine, Naive Bayes Classifier and Random Forest, Recursive Feature Addition outperformed other methods. Our studies also showed that Lagging Prediction Peephole Optimization is superior to random strategy; Recursive Feature Addition with Lagging Prediction Peephole Optimization obtained better testing accuracies than the gene selection method varSelRF.</p

Supervised learning-based tagSNP selection for genome-wide disease classifications

The article was originally published by BMC Genomics. doi:10.1186/1471-2164-9-S1-S6Comprehensive evaluation of common genetic variations through association of single nucleotide polymorphisms (SNPs) with complex human diseases on the genome-wide scale is an active area in human genome research. One of the fundamental questions in a SNP-disease association study is to find an optimal subset of SNPs with predicting power for disease status. To find that subset while reducing study burden in terms of time and costs, one can potentially reconcile information redundancy from associations between SNP markersResearch supports received from ICASA (Institute for Complex Additive Systems Analysis, a division of New Mexico Tech) and the Radiology Department of Brigham and Women's Hospital (BWH) are gratefully acknowledged. The authors highly appreciate Dr. Liang at SUNY-Buffalo for her invaluable help and insightful discussion during this study and Ms. Kim Lawson at BWH Radiology Department for her manuscript editing and very constructive comments.Supervised Recursive Feature AdditionsSupport Vector bases Recursive Feature Additioncomplex diseasegeneticsdisease prediction

Independent component analysis of Alzheimer's DNA microarray gene expression data

<p>Abstract</p> <p>Background</p> <p>Gene microarray technology is an effective tool to investigate the simultaneous activity of multiple cellular pathways from hundreds to thousands of genes. However, because data in the colossal amounts generated by DNA microarray technology are usually complex, noisy, high-dimensional, and often hindered by low statistical power, their exploitation is difficult. To overcome these problems, two kinds of unsupervised analysis methods for microarray data: principal component analysis (PCA) and independent component analysis (ICA) have been developed to accomplish the task. PCA projects the data into a new space spanned by the principal components that are mutually orthonormal to each other. The constraint of mutual orthogonality and second-order statistics technique within PCA algorithms, however, may not be applied to the biological systems studied. Extracting and characterizing the most informative features of the biological signals, however, require higher-order statistics.</p> <p>Results</p> <p>ICA is one of the unsupervised algorithms that can extract higher-order statistical structures from data and has been applied to DNA microarray gene expression data analysis. We performed FastICA method on DNA microarray gene expression data from Alzheimer's disease (AD) hippocampal tissue samples and consequential gene clustering. Experimental results showed that the ICA method can improve the clustering results of AD samples and identify significant genes. More than 50 significant genes with high expression levels in severe AD were extracted, representing immunity-related protein, metal-related protein, membrane protein, lipoprotein, neuropeptide, cytoskeleton protein, cellular binding protein, and ribosomal protein. Within the aforementioned categories, our method also found 37 significant genes with low expression levels. Moreover, it is worth noting that some oncogenes and phosphorylation-related proteins are expressed in low levels. In comparison to the PCA and support vector machine recursive feature elimination (SVM-RFE) methods, which are widely used in microarray data analysis, ICA can identify more AD-related genes. Furthermore, we have validated and identified many genes that are associated with AD pathogenesis.</p> <p>Conclusion</p> <p>We demonstrated that ICA exploits higher-order statistics to identify gene expression profiles as linear combinations of elementary expression patterns that lead to the construction of potential AD-related pathogenic pathways. Our computing results also validated that the ICA model outperformed PCA and the SVM-RFE method. This report shows that ICA as a microarray data analysis tool can help us to elucidate the molecular taxonomy of AD and other multifactorial and polygenic complex diseases.</p

Size-dependent tissue-specific biological effects of core-shell structured Fe3O4@SiO2-NH2 nanoparticles.

BACKGROUND(#br)Understanding the in vivo size-dependent pharmacokinetics and toxicity of nanoparticles is crucial to determine their successful development. Systematic studies on the size-dependent biological effects of nanoparticles not only help to unravel unknown toxicological mechanism but also contribute to the possible biological applications of nanomaterial.(#br)METHODS(#br)In this study, the biodistribution and the size-dependent biological effects of Fe3O4@SiO2-NH2 nanoparticles (Fe@Si-NPs) in three diameters (10, 20 and 40 nm) were investigated by ICP-AES, serum biochemistry analysis and NMR-based metabolomic analysis after intravenous administration in a rat model.(#br)RESULTS(#br)Our findings indicated that biodistribution and biological activities of Fe@Si-NPs demonstrated the obvious size-dependent and tissue-specific effects. Spleen and liver are the target tissues of Fe@Si-NPs, and 20 nm of Fe@Si-NPs showed a possible longer blood circulation time. Quantitative biochemical analysis showed that the alterations of lactate dehydrogenase (LDH) and uric acid (UA) were correlated to some extent with the sizes of Fe@Si-NPs. The untargeted metabolomic analyses of tissue metabolomes (kidney, liver, lung, and spleen) indicated that different sizes of Fe@Si-NPs were involved in the different biochemical mechanisms. LDH, formate, uric acid, and GSH related metabolites were suggested as sensitive indicators for the size-dependent toxic effects of Fe@Si-NPs. The findings from serum biochemical analysis and metabolomic analysis corroborate each other. Thus we proposed a toxicity hypothesis that size-dependent NAD depletion may occur in vivo in response to nanoparticle exposure. To our knowledge, this is the first report that links size-dependent biological effects of nanoparticles with in vivo NAD depletion in rats.(#br)CONCLUSION(#br)The integrated metabolomic approach is an effective tool to understand physiological responses to the size-specific properties of nanoparticles. Our results can provide a direction for the future biological applications of Fe@Si-NPs

Comparison of feature selection and classification for MALDI-MS data

INTRODUCTION: In the classification of Mass Spectrometry (MS) proteomics data, peak detection, feature selection, and learning classifiers are critical to classification accuracy. To better understand which methods are more accurate when classifying data, some publicly available peak detection algorithms for Matrix assisted Laser Desorption Ionization Mass Spectrometry (MALDI-MS) data were recently compared; however, the issue of different feature selection methods and different classification models as they relate to classification performance has not been addressed. With the application of intelligent computing, much progress has been made in the development of feature selection methods and learning classifiers for the analysis of high-throughput biological data. The main objective of this paper is to compare the methods of feature selection and different learning classifiers when applied to MALDI-MS data and to provide a subsequent reference for the analysis of MS proteomics data. RESULTS: We compared a well-known method of feature selection, Support Vector Machine Recursive Feature Elimination (SVMRFE), and a recently developed method, Gradient based Leave-one-out Gene Selection (GLGS) that effectively performs microarray data analysis. We also compared several learning classifiers including K-Nearest Neighbor Classifier (KNNC), Naïve Bayes Classifier (NBC), Nearest Mean Scaled Classifier (NMSC), uncorrelated normal based quadratic Bayes Classifier recorded as UDC, Support Vector Machines, and a distance metric learning for Large Margin Nearest Neighbor classifier (LMNN) based on Mahanalobis distance. To compare, we conducted a comprehensive experimental study using three types of MALDI-MS data. CONCLUSION: Regarding feature selection, SVMRFE outperformed GLGS in classification. As for the learning classifiers, when classification models derived from the best training were compared, SVMs performed the best with respect to the expected testing accuracy. However, the distance metric learning LMNN outperformed SVMs and other classifiers on evaluating the best testing. In such cases, the optimum classification model based on LMNN is worth investigating for future study