Abstract:
:An important application of gene expression microarray data is classification of biological samples or prediction of clinical and other outcomes. One necessary part of multivariate statistical analysis in such applications is dimension reduction. This paper provides a comparison study of three dimension reduction techniques, namely partial least squares (PLS), sliced inverse regression (SIR) and principal component analysis (PCA), and evaluates the relative performance of classification procedures incorporating those methods. A five-step assessment procedure is designed for the purpose. Predictive accuracy and computational efficiency of the methods are examined. Two gene expression data sets for tumor classification are used in the study.
journal_name
Stat Appl Genet Mol Biolauthors
Dai JJ,Lieu L,Rocke Ddoi
10.2202/1544-6115.1147subject
Has Abstractpub_date
2006-01-01 00:00:00pages
Article6eissn
2194-6302issn
1544-6115journal_volume
5pub_type
杂志文章abstract::Multiple testing procedures are commonly used in gene expression studies for the detection of differential expression, where typically thousands of genes are measured over at least two experimental conditions. Given the need for powerful testing procedures, and the attendant danger of false positives in multiple testi...
journal_title:Statistical applications in genetics and molecular biology
pub_type: 杂志文章
doi:10.2202/1544-6115.1302
更新日期:2007-01-01 00:00:00
abstract::The genetic control of a complex trait can be studied by testing and mapping the genotypes of the underlying quantitative trait loci (QTLs) through their associations with observable marker genotypes. All existing statistical methods for QTL mapping assume an equilibrium population, allowing marker-QTL associations to...
journal_title:Statistical applications in genetics and molecular biology
pub_type: 杂志文章
doi:10.2202/1544-6115.1578
更新日期:2010-01-01 00:00:00
abstract::Several important syndromes are caused by deleterious germline mutations of individual genes. In both clinical and research applications it is useful to evaluate the probability that an individual carries an inherited genetic variant of these genes, and to predict the risk of disease for that individual, using informa...
journal_title:Statistical applications in genetics and molecular biology
pub_type: 杂志文章
doi:10.2202/1544-6115.1063
更新日期:2004-01-01 00:00:00
abstract::In this paper, we address the problem of detecting outlier samples with highly different expression patterns in microarray data. Although outliers are not common, they appear even in widely used benchmark data sets and can negatively affect microarray data analysis. It is important to identify outliers in order to exp...
journal_title:Statistical applications in genetics and molecular biology
pub_type: 杂志文章
doi:10.2202/1544-6115.1426
更新日期:2009-01-01 00:00:00
abstract::Certain residues have no known function yet are co-conserved across distantly related protein families and diverse organisms, suggesting that they perform critical roles associated with as-yet-unidentified molecular properties and mechanisms. This raises the question of how to obtain additional clues regarding these m...
journal_title:Statistical applications in genetics and molecular biology
pub_type: 杂志文章
doi:10.2202/1544-6115.1666
更新日期:2011-01-01 00:00:00
abstract::We present a Bayesian hierarchical model for detecting differentially expressed genes using a mixture prior on the parameters representing differential effects. We formulate an easily interpretable 3-component mixture to classify genes as over-expressed, under-expressed and non-differentially expressed, and model gene...
journal_title:Statistical applications in genetics and molecular biology
pub_type: 杂志文章
doi:10.2202/1544-6115.1314
更新日期:2007-01-01 00:00:00
abstract::Recent analytic and technological breakthroughs have set the stage for genome-wide linkage disequilibrium studies to map disease-susceptibility variants. This paper discusses a probabilistic methodology for making disease-mapping inferences in large-scale case-control genetic studies. The semi-Bayesian approach promot...
journal_title:Statistical applications in genetics and molecular biology
pub_type: 杂志文章
doi:10.2202/1544-6115.1168
更新日期:2005-01-01 00:00:00
abstract::The approach adopted involved two-stages. First the 11205 measurements in the mass spectrometry data were reduced to 14 scores by a principal component analysis of the centered but otherwise untreated and unscaled data matrix. Then a linear classifier was derived by linear discriminant analysis using these 14 scores a...
journal_title:Statistical applications in genetics and molecular biology
pub_type: 杂志文章
doi:10.2202/1544-6115.1350
更新日期:2008-01-01 00:00:00
abstract::In many population genetic problems, parameter estimation is obstructed by an intractable likelihood function. Therefore, approximate estimation methods have been developed, and with growing computational power, sampling-based methods became popular. However, these methods such as Approximate Bayesian Computation (ABC...
journal_title:Statistical applications in genetics and molecular biology
pub_type: 杂志文章
doi:10.1515/sagmb-2017-0016
更新日期:2017-11-27 00:00:00
abstract::Likelihood-based cross-validation is a statistical tool for selecting a density estimate based on n i.i.d. observations from the true density among a collection of candidate density estimators. General examples are the selection of a model indexing a maximum likelihood estimator, and the selection of a bandwidth index...
journal_title:Statistical applications in genetics and molecular biology
pub_type: 杂志文章
doi:10.2202/1544-6115.1036
更新日期:2004-01-01 00:00:00
abstract::Integrative analysis of copy number and gene expression data can help in understanding the cis and trans effect of copy number aberrations on transcription levels of genes involved in a pathway. To analyse how these copy number mediated gene-gene interactions differ between groups of samples we propose a new method, n...
journal_title:Statistical applications in genetics and molecular biology
pub_type: 杂志文章
doi:10.1515/sagmb-2017-0058
更新日期:2018-07-31 00:00:00
abstract::In recent years, alignment-free methods have been widely applied in comparing genome sequences, as these methods compute efficiently and provide desirable phylogenetic analysis results. These methods have been successfully combined with hierarchical clustering methods for finding phylogenetic trees. However, it may no...
journal_title:Statistical applications in genetics and molecular biology
pub_type: 杂志文章
doi:10.1515/sagmb-2018-0045
更新日期:2019-02-15 00:00:00
abstract::Germline mosaicism is a genetic condition in which some germ cells of an individual contain a mutation. This condition violates the assumptions underlying classic genetic analysis and may lead to failure of such analysis. In this work we extend the statistical model used for genetic linkage analysis in order to incorp...
journal_title:Statistical applications in genetics and molecular biology
pub_type: 杂志文章
doi:10.2202/1544-6115.1709
更新日期:2011-10-04 00:00:00
abstract::Consider the standard multiple testing problem where many hypotheses are to be tested, each hypothesis is associated with a test statistic, and large test statistics provide evidence against the null hypotheses. One proposal to provide probabilistic control of Type-I errors is the use of procedures ensuring that the e...
journal_title:Statistical applications in genetics and molecular biology
pub_type: 杂志文章
doi:10.2202/1544-6115.1148
更新日期:2006-01-01 00:00:00
abstract::In candidate gene association studies, usually several elementary hypotheses are tested simultaneously using one particular set of data. The data normally consist of partly correlated SNP information. Every SNP can be tested for association with the disease, e.g., using the Cochran-Armitage test for trend. To account ...
journal_title:Statistical applications in genetics and molecular biology
pub_type: 杂志文章
doi:10.2202/1544-6115.1729
更新日期:2011-01-01 00:00:00
abstract::Gene microarray technology is often used to compare the expression of thousand of genes in two different cell lines. Typically, one does not expect measurable changes in transcription amounts for a large number of genes; furthermore, the noise level of array experiments is rather high in relation to the available numb...
journal_title:Statistical applications in genetics and molecular biology
pub_type: 杂志文章
doi:10.2202/1544-6115.1132
更新日期:2005-01-01 00:00:00
abstract::In a hidden Markov model, one "estimates" the state of the hidden Markov chain at t by computing via the forwards-backwards algorithm the conditional distribution of the state vector given the observed data. The covariance matrix of this conditional distribution measures the information lost by failure to observe dire...
journal_title:Statistical applications in genetics and molecular biology
pub_type: 杂志文章,评审
doi:10.2202/1544-6115.1296
更新日期:2007-01-01 00:00:00
abstract::Usually, a pedigree is sampled and included in the sample that is analyzed after following a predefined non-random sampling design comprising several specific procedures. To obtain a pedigree analysis result free from the bias caused by the sampling procedures, a correction is applied to the pedigree likelihood. The s...
journal_title:Statistical applications in genetics and molecular biology
pub_type: 杂志文章
doi:10.2202/1544-6115.1003
更新日期:2003-01-01 00:00:00
abstract::The Dirichlet Process (DP) mixture model has become a popular choice for model-based clustering, largely because it allows the number of clusters to be inferred. The sequential updating and greedy search (SUGS) algorithm (Wang & Dunson, 2011) was proposed as a fast method for performing approximate Bayesian inference ...
journal_title:Statistical applications in genetics and molecular biology
pub_type: 杂志文章
doi:10.1515/sagmb-2018-0065
更新日期:2019-12-12 00:00:00
abstract::Reproducibility of disease signatures and clinical biomarkers in multi-omics disease analysis has been a key challenge due to a multitude of factors. The heterogeneity of the limited sample, various biological factors such as environmental confounders, and the inherent experimental and technical noises, compounded wit...
journal_title:Statistical applications in genetics and molecular biology
pub_type: 杂志文章
doi:10.1515/sagmb-2018-0039
更新日期:2019-05-11 00:00:00
abstract::We are concerned with statistical inference for 2 × C × K contingency tables in the context of genetic case-control association studies. Multivariate methods based on asymptotic Gaussianity of vectors of test statistics require information about the asymptotic correlation structure among these test statistics under th...
journal_title:Statistical applications in genetics and molecular biology
pub_type: 杂志文章
doi:10.1515/sagmb-2015-0024
更新日期:2015-11-01 00:00:00
abstract::High-throughput sequencing techniques are increasingly affordable and produce massive amounts of data. Together with other high-throughput technologies, such as microarrays, there are an enormous amount of resources in databases. The collection of these valuable data has been routine for more than a decade. Despite di...
journal_title:Statistical applications in genetics and molecular biology
pub_type: 杂志文章
doi:10.1515/sagmb-2014-0093
更新日期:2015-06-01 00:00:00
abstract::Combining correlated p-values from multiple hypothesis testing is a most frequently used method for integrating information in genetic and genomic data analysis. However, most existing methods for combining independent p-values from individual component problems into a single unified p-value are unsuitable for the cor...
journal_title:Statistical applications in genetics and molecular biology
pub_type: 杂志文章
doi:10.1515/sagmb-2019-0057
更新日期:2020-11-06 00:00:00
abstract::Output from analysis of a high-throughput 'omics' experiment very often is a ranked list. One commonly encountered example is a ranked list of differentially expressed genes from a gene expression experiment, with a length of many hundreds of genes. There are numerous situations where interest is in the comparison of ...
journal_title:Statistical applications in genetics and molecular biology
pub_type: 杂志文章
doi:10.1515/sagmb-2016-0036
更新日期:2017-03-01 00:00:00
abstract::Gametic models for fitting breeding values at QTL as random effects in outbred populations have become popular because they require few assumptions about the number and distribution of QTL alleles segregating. The covariance matrix of the gametic effects has an inverse that is sparse and can be constructed rapidly by ...
journal_title:Statistical applications in genetics and molecular biology
pub_type: 杂志文章
doi:10.2202/1544-6115.1048
更新日期:2004-01-01 00:00:00
abstract::In this study, we propose a novel statistical framework for detecting progressive changes in molecular traits as response to a pathogenic stimulus. In particular, we propose to employ Bayesian hierarchical models to analyse changes in mean level, variance and correlation of metabolic traits in relation to covariates. ...
journal_title:Statistical applications in genetics and molecular biology
pub_type: 杂志文章
doi:10.1515/sagmb-2013-0041
更新日期:2014-04-01 00:00:00
abstract::The ENCODE project has funded the generation of a diverse collection of methylation profiles using reduced representation bisulfite sequencing (RRBS) technology, enabling the analysis of epigenetic variation on a genomic scale at single-site resolution. A standard application of RRBS experiments is in the location of ...
journal_title:Statistical applications in genetics and molecular biology
pub_type: 杂志文章
doi:10.1515/sagmb-2013-0027
更新日期:2013-12-01 00:00:00
abstract::Many gene- and pathway-based association tests have been proposed in the literature. Among them, the SKAT is widely used, especially for rare variants association studies. In this paper, we investigate the connection between SKAT and a principal component analysis. This investigation leads to a procedure that encompas...
journal_title:Statistical applications in genetics and molecular biology
pub_type: 杂志文章
doi:10.1515/sagmb-2016-0061
更新日期:2017-07-26 00:00:00
abstract::Accurately measuring epigenetic marks such as 5-methylcytosine (5-mC) and 5-hydroxymethylcytosine (5-hmC) at the single-nucleotide level, requires combining data from DNA processing methods including traditional (BS), oxidative (oxBS) or Tet-Assisted (TAB) bisulfite conversion. We introduce the R package MLML2R, which...
journal_title:Statistical applications in genetics and molecular biology
pub_type: 杂志文章
doi:10.1515/sagmb-2018-0031
更新日期:2019-01-17 00:00:00
abstract::Locus heterogeneity is one of the most important issues in gene mapping and can cause significant reductions in statistical power for gene mapping, yet no research to date has provided power and sample size calculations for family-based association methods in the presence of locus heterogeneity. The purpose of this re...
journal_title:Statistical applications in genetics and molecular biology
pub_type: 杂志文章
doi:10.2202/1544-6115.1501
更新日期:2009-01-01 00:00:00